Starting phenix.real_space_refine on Sun Dec 10 00:45:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osh_13051/12_2023/7osh_13051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osh_13051/12_2023/7osh_13051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osh_13051/12_2023/7osh_13051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osh_13051/12_2023/7osh_13051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osh_13051/12_2023/7osh_13051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osh_13051/12_2023/7osh_13051.pdb" } resolution = 3.8 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 Cu 1 5.60 5 Mg 1 5.21 5 S 45 5.16 5 C 8200 2.51 5 N 2249 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H GLU 138": "OE1" <-> "OE2" Residue "H ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3077 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2375 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain: "C" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 12, 'TRANS': 294} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1092 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11839 SG CYS H 45 45.430 43.120 48.151 1.00133.21 S ATOM 11862 SG CYS H 48 43.343 44.213 45.789 1.00130.17 S ATOM 12043 SG CYS H 72 46.172 45.161 44.243 1.00137.89 S Time building chain proxies: 7.20, per 1000 atoms: 0.56 Number of scatterers: 12826 At special positions: 0 Unit cell: (80.352, 92.016, 193.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cu 1 28.99 S 45 16.00 Mg 1 11.99 O 2329 8.00 N 2249 7.00 C 8200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.23 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 48 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 72 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 13 sheets defined 44.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.535A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.507A pdb=" N MET A 390 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.645A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.851A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.595A pdb=" N GLN B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.743A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 233 through 244 removed outlier: 4.406A pdb=" N ARG B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.013A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.624A pdb=" N TYR B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.519A pdb=" N MET C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 107 through 114 removed outlier: 3.881A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.616A pdb=" N GLN C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.828A pdb=" N GLN C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 273 removed outlier: 3.644A pdb=" N LEU C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.568A pdb=" N ALA C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.155A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.524A pdb=" N GLY D 34 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.658A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.784A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.108A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.519A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.869A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.620A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.993A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 3.637A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.756A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.644A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.648A pdb=" N ALA E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.586A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.549A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.787A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 removed outlier: 3.501A pdb=" N PHE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.535A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 207 through 213 removed outlier: 4.044A pdb=" N TRP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.516A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.233A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 55 removed outlier: 3.803A pdb=" N ASP H 54 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 160 through 172 removed outlier: 3.681A pdb=" N GLN H 165 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 7.937A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.797A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.591A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.653A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.332A pdb=" N LEU A 216 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 25 removed outlier: 5.368A pdb=" N HIS B 20 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN B 11 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU B 24 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN B 7 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.703A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 31 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA B 199 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY B 33 " --> pdb=" O ALA B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 251 removed outlier: 6.692A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.791A pdb=" N VAL C 4 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.782A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 228 removed outlier: 3.676A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.523A pdb=" N VAL H 121 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG H 152 " --> pdb=" O VAL H 121 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1491 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: 3.61 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4182 1.34 - 1.46: 2340 1.46 - 1.57: 6466 1.57 - 1.69: 2 1.69 - 1.81: 77 Bond restraints: 13067 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.586 -0.061 2.10e-02 2.27e+03 8.35e+00 bond pdb=" CG1 ILE B 181 " pdb=" CD1 ILE B 181 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.24e+00 bond pdb=" CB VAL A 202 " pdb=" CG1 VAL A 202 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.34e+00 bond pdb=" CB GLN A 232 " pdb=" CG GLN A 232 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.99e+00 bond pdb=" CB TYR A 291 " pdb=" CG TYR A 291 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.20e-02 2.07e+03 4.61e+00 ... (remaining 13062 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.50: 231 105.50 - 112.80: 6799 112.80 - 120.10: 5310 120.10 - 127.41: 5220 127.41 - 134.71: 166 Bond angle restraints: 17726 Sorted by residual: angle pdb=" CA LEU A 356 " pdb=" CB LEU A 356 " pdb=" CG LEU A 356 " ideal model delta sigma weight residual 116.30 133.64 -17.34 3.50e+00 8.16e-02 2.46e+01 angle pdb=" C GLU H 64 " pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 125.02 133.63 -8.61 1.76e+00 3.23e-01 2.39e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 122.07 128.93 -6.86 1.43e+00 4.89e-01 2.30e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C GLU H 138 " pdb=" N GLU H 139 " pdb=" CA GLU H 139 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 ... (remaining 17721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 6835 16.98 - 33.97: 714 33.97 - 50.95: 162 50.95 - 67.93: 18 67.93 - 84.92: 7 Dihedral angle restraints: 7736 sinusoidal: 3041 harmonic: 4695 Sorted by residual: dihedral pdb=" CA ASP H 108 " pdb=" C ASP H 108 " pdb=" N GLY H 109 " pdb=" CA GLY H 109 " ideal model delta harmonic sigma weight residual 180.00 148.88 31.12 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA ARG C 233 " pdb=" C ARG C 233 " pdb=" N ASP C 234 " pdb=" CA ASP C 234 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual 180.00 -157.01 -22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 7733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1704 0.082 - 0.164: 277 0.164 - 0.245: 41 0.245 - 0.327: 5 0.327 - 0.409: 3 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN C 261 " pdb=" N ASN C 261 " pdb=" C ASN C 261 " pdb=" CB ASN C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2027 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 209 " -0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO E 210 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO D 67 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO E 67 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.041 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 120 2.56 - 3.14: 9266 3.14 - 3.73: 20139 3.73 - 4.31: 28354 4.31 - 4.90: 46659 Nonbonded interactions: 104538 Sorted by model distance: nonbonded pdb=" OE1 GLU H 76 " pdb="ZN ZN H 201 " model vdw 1.971 2.230 nonbonded pdb=" NE2 HIS A 207 " pdb="CU CU A 502 " model vdw 2.002 2.320 nonbonded pdb=" SD MET H 50 " pdb="CU CU A 502 " model vdw 2.113 2.600 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.129 2.170 nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 2.157 2.170 ... (remaining 104533 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 'B' and resid 2 through 308) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } 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: 0.330 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: 2.450 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.140 Find NCS groups from input model: 0.650 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 0.008 0.097 13067 Z= 0.548 Angle : 1.089 17.345 17726 Z= 0.575 Chirality : 0.065 0.409 2030 Planarity : 0.007 0.096 2276 Dihedral : 14.372 84.915 4740 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.60 % Allowed : 10.05 % Favored : 89.35 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.50 (0.14), residues: 1645 helix: -4.39 (0.08), residues: 697 sheet: -2.98 (0.29), residues: 235 loop : -2.90 (0.19), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 211 HIS 0.013 0.002 HIS C 37 PHE 0.018 0.003 PHE D 157 TYR 0.014 0.002 TYR C 13 ARG 0.006 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 147 average time/residue: 0.3521 time to fit residues: 68.8198 Evaluate side-chains 82 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1063 time to fit residues: 2.0912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 0.0070 chunk 77 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN B 20 HIS B 37 HIS B 38 ASN B 176 GLN C 25 ASN ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 238 GLN C 270 GLN D 225 ASN E 108 HIS E 225 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13067 Z= 0.153 Angle : 0.576 10.233 17726 Z= 0.296 Chirality : 0.042 0.172 2030 Planarity : 0.005 0.059 2276 Dihedral : 4.935 21.923 1803 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.12 % Allowed : 13.70 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.35 (0.18), residues: 1645 helix: -1.85 (0.16), residues: 711 sheet: -2.42 (0.29), residues: 253 loop : -2.40 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 253 HIS 0.005 0.001 HIS C 37 PHE 0.010 0.001 PHE A 303 TYR 0.015 0.001 TYR B 86 ARG 0.004 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 116 average time/residue: 0.2331 time to fit residues: 41.2773 Evaluate side-chains 85 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1144 time to fit residues: 2.8248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 160 optimal weight: 0.0020 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 38 ASN D 225 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13067 Z= 0.145 Angle : 0.544 9.885 17726 Z= 0.273 Chirality : 0.041 0.166 2030 Planarity : 0.004 0.048 2276 Dihedral : 4.496 21.799 1803 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.04 % Allowed : 16.01 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.20), residues: 1645 helix: -0.20 (0.19), residues: 713 sheet: -2.18 (0.30), residues: 263 loop : -2.17 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 211 HIS 0.004 0.000 HIS C 194 PHE 0.010 0.001 PHE D 157 TYR 0.009 0.001 TYR H 118 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 116 average time/residue: 0.2412 time to fit residues: 42.1480 Evaluate side-chains 88 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.484 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1159 time to fit residues: 3.1745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 77 optimal weight: 0.0000 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 120 HIS D 225 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13067 Z= 0.209 Angle : 0.555 8.938 17726 Z= 0.281 Chirality : 0.042 0.161 2030 Planarity : 0.003 0.042 2276 Dihedral : 4.370 18.954 1803 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.27 % Allowed : 17.13 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1645 helix: 0.62 (0.20), residues: 722 sheet: -2.02 (0.29), residues: 278 loop : -2.10 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 211 HIS 0.006 0.001 HIS C 194 PHE 0.013 0.001 PHE D 157 TYR 0.021 0.001 TYR H 118 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 102 average time/residue: 0.2537 time to fit residues: 38.5404 Evaluate side-chains 84 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1165 time to fit residues: 3.2257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 ASN D 225 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13067 Z= 0.373 Angle : 0.666 7.912 17726 Z= 0.332 Chirality : 0.044 0.161 2030 Planarity : 0.004 0.036 2276 Dihedral : 4.688 21.424 1803 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.41 % Allowed : 18.17 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1645 helix: 0.95 (0.20), residues: 721 sheet: -2.02 (0.31), residues: 257 loop : -1.99 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 211 HIS 0.010 0.001 HIS C 194 PHE 0.020 0.002 PHE D 157 TYR 0.014 0.002 TYR B 86 ARG 0.003 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 4.264 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.2469 time to fit residues: 35.6833 Evaluate side-chains 83 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1175 time to fit residues: 3.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.1980 chunk 141 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 157 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13067 Z= 0.138 Angle : 0.550 9.183 17726 Z= 0.275 Chirality : 0.041 0.162 2030 Planarity : 0.003 0.036 2276 Dihedral : 4.251 20.080 1803 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.12 % Allowed : 19.06 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.22), residues: 1645 helix: 1.43 (0.21), residues: 718 sheet: -1.75 (0.30), residues: 280 loop : -1.81 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 253 HIS 0.004 0.001 HIS C 194 PHE 0.008 0.001 PHE D 157 TYR 0.012 0.001 TYR H 118 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.559 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 105 average time/residue: 0.2447 time to fit residues: 38.8465 Evaluate side-chains 87 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1652 time to fit residues: 4.2600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13067 Z= 0.322 Angle : 0.627 7.762 17726 Z= 0.312 Chirality : 0.044 0.151 2030 Planarity : 0.003 0.036 2276 Dihedral : 4.432 20.061 1803 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.89 % Allowed : 19.51 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.22), residues: 1645 helix: 1.46 (0.21), residues: 724 sheet: -1.86 (0.31), residues: 272 loop : -1.82 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 211 HIS 0.007 0.001 HIS D 108 PHE 0.017 0.002 PHE D 157 TYR 0.012 0.002 TYR B 13 ARG 0.003 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.622 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.2446 time to fit residues: 32.6874 Evaluate side-chains 80 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1255 time to fit residues: 3.4215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13067 Z= 0.147 Angle : 0.558 8.707 17726 Z= 0.277 Chirality : 0.041 0.166 2030 Planarity : 0.003 0.039 2276 Dihedral : 4.191 19.355 1803 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.60 % Allowed : 19.51 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.22), residues: 1645 helix: 1.72 (0.21), residues: 724 sheet: -1.77 (0.31), residues: 271 loop : -1.76 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 253 HIS 0.005 0.001 HIS C 194 PHE 0.010 0.001 PHE D 157 TYR 0.012 0.001 TYR H 118 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.561 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 95 average time/residue: 0.2464 time to fit residues: 35.5486 Evaluate side-chains 81 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1164 time to fit residues: 2.3653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0060 chunk 146 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13067 Z= 0.144 Angle : 0.557 9.391 17726 Z= 0.275 Chirality : 0.041 0.196 2030 Planarity : 0.003 0.035 2276 Dihedral : 4.075 19.987 1803 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.37 % Allowed : 20.33 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1645 helix: 1.88 (0.21), residues: 722 sheet: -1.70 (0.31), residues: 271 loop : -1.67 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 236 HIS 0.004 0.001 HIS C 37 PHE 0.010 0.001 PHE D 157 TYR 0.010 0.001 TYR H 118 ARG 0.002 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 94 average time/residue: 0.2625 time to fit residues: 37.3447 Evaluate side-chains 81 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13067 Z= 0.325 Angle : 0.643 9.221 17726 Z= 0.318 Chirality : 0.044 0.190 2030 Planarity : 0.003 0.038 2276 Dihedral : 4.365 18.964 1803 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.37 % Allowed : 20.70 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.22), residues: 1645 helix: 1.72 (0.21), residues: 723 sheet: -1.81 (0.31), residues: 266 loop : -1.63 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 211 HIS 0.005 0.001 HIS C 37 PHE 0.016 0.001 PHE D 157 TYR 0.018 0.002 TYR H 94 ARG 0.003 0.000 ARG C 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.673 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 0.2710 time to fit residues: 33.0798 Evaluate side-chains 73 residues out of total 1343 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1199 time to fit residues: 2.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.6980 chunk 39 optimal weight: 0.0470 chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 165 GLN ** 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 = 0.3147 r_free = 0.3147 target = 0.055282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044911 restraints weight = 53296.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046579 restraints weight = 26203.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047715 restraints weight = 16502.708| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13067 Z= 0.151 Angle : 0.562 8.960 17726 Z= 0.278 Chirality : 0.042 0.196 2030 Planarity : 0.003 0.034 2276 Dihedral : 4.139 18.416 1803 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.07 % Allowed : 20.85 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.22), residues: 1645 helix: 1.88 (0.21), residues: 722 sheet: -1.71 (0.32), residues: 266 loop : -1.59 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 253 HIS 0.004 0.001 HIS C 194 PHE 0.009 0.001 PHE D 157 TYR 0.013 0.001 TYR B 86 ARG 0.002 0.000 ARG H 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2133.87 seconds wall clock time: 40 minutes 3.98 seconds (2403.98 seconds total)