Starting phenix.real_space_refine on Fri Dec 8 23:45:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/12_2023/6wwz_21950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/12_2023/6wwz_21950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/12_2023/6wwz_21950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/12_2023/6wwz_21950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/12_2023/6wwz_21950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/12_2023/6wwz_21950.pdb" } resolution = 3.34 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= 0.003 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6026 2.51 5 N 1612 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "Y ARG 62": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R ARG 286": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9450 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 530 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Y" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1649 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "S" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1770 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2468 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 301} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 5.24, per 1000 atoms: 0.55 Number of scatterers: 9450 At special positions: 0 Unit cell: (116.58, 121.8, 157.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1742 8.00 N 1612 7.00 C 6026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 32 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.05 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 36 " - pdb=" SG CYS R 288 " distance=2.04 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 197 " distance=2.04 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: 3.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 3 through 22 removed outlier: 3.845A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.935A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.628A pdb=" N LEU C 62 " --> pdb=" O TYR C 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 22 Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.635A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Y 43 " --> pdb=" O ALA Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.695A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.536A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.877A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.544A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 283 through 287 removed outlier: 4.005A pdb=" N ILE A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 296 through 299 removed outlier: 4.179A pdb=" N ASP A 299 " --> pdb=" O THR A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.807A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.677A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 73 removed outlier: 3.943A pdb=" N LEU R 47 " --> pdb=" O GLN R 43 " (cutoff:3.500A) Proline residue: R 50 - end of helix removed outlier: 3.938A pdb=" N LEU R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL R 67 " --> pdb=" O GLY R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 98 removed outlier: 3.550A pdb=" N TYR R 84 " --> pdb=" O MET R 80 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU R 94 " --> pdb=" O ILE R 90 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 109 removed outlier: 4.290A pdb=" N ALA R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 149 removed outlier: 3.564A pdb=" N CYS R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS R 122 " --> pdb=" O CYS R 118 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY R 123 " --> pdb=" O LYS R 119 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE R 127 " --> pdb=" O GLY R 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET R 133 " --> pdb=" O PHE R 129 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU R 134 " --> pdb=" O ASN R 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU R 135 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN R 149 " --> pdb=" O ILE R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 157 Processing helix chain 'R' and resid 160 through 185 removed outlier: 4.288A pdb=" N SER R 164 " --> pdb=" O THR R 160 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE R 166 " --> pdb=" O PRO R 162 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER R 181 " --> pdb=" O ILE R 177 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR R 182 " --> pdb=" O ILE R 178 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE R 185 " --> pdb=" O SER R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 242 removed outlier: 3.930A pdb=" N TRP R 210 " --> pdb=" O GLU R 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU R 218 " --> pdb=" O MET R 214 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 221 " --> pdb=" O LEU R 217 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) Proline residue: R 226 - end of helix removed outlier: 3.511A pdb=" N PHE R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR R 240 " --> pdb=" O PHE R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 280 removed outlier: 3.812A pdb=" N ALA R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE R 253 " --> pdb=" O ARG R 249 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG R 254 " --> pdb=" O HIS R 250 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU R 264 " --> pdb=" O VAL R 260 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) Proline residue: R 269 - end of helix removed outlier: 3.723A pdb=" N ALA R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 320 removed outlier: 3.714A pdb=" N GLU R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR R 299 " --> pdb=" O GLY R 295 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL R 303 " --> pdb=" O THR R 299 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE R 306 " --> pdb=" O GLU R 302 " (cutoff:3.500A) Proline residue: R 313 - end of helix removed outlier: 3.878A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 335 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.834A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.906A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.606A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.711A pdb=" N CYS B 149 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N SER B 160 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 151 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 158 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.114A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.805A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.697A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.677A pdb=" N GLY C 22 " --> pdb=" O HIS C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.548A pdb=" N PHE A 190 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.557A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.575A pdb=" N CYS S 147 " --> pdb=" O PHE S 200 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 135 removed outlier: 6.826A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 186 through 189 removed outlier: 3.537A pdb=" N GLN R 187 " --> pdb=" O GLU R 198 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU R 198 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR R 189 " --> pdb=" O VAL R 196 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1092 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: 2.67 Time building geometry restraints manager: 3.54 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: 1915 1.34 - 1.46: 2249 1.46 - 1.58: 5380 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 9641 Sorted by residual: bond pdb=" N VAL B 276 " pdb=" CA VAL B 276 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.49e+01 bond pdb=" N VAL S 137 " pdb=" CA VAL S 137 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" N ASN R 312 " pdb=" CA ASN R 312 " ideal model delta sigma weight residual 1.462 1.491 -0.029 7.70e-03 1.69e+04 1.45e+01 bond pdb=" N ILE B 269 " pdb=" CA ILE B 269 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.19e-02 7.06e+03 1.39e+01 bond pdb=" N LEU R 99 " pdb=" CA LEU R 99 " ideal model delta sigma weight residual 1.462 1.493 -0.031 8.50e-03 1.38e+04 1.33e+01 ... (remaining 9636 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.30: 194 106.30 - 113.33: 5003 113.33 - 120.37: 4373 120.37 - 127.41: 3410 127.41 - 134.45: 69 Bond angle restraints: 13049 Sorted by residual: angle pdb=" N GLU A 217 " pdb=" CA GLU A 217 " pdb=" C GLU A 217 " ideal model delta sigma weight residual 111.28 120.08 -8.80 1.09e+00 8.42e-01 6.51e+01 angle pdb=" C CYS A 287 " pdb=" N PHE A 288 " pdb=" CA PHE A 288 " ideal model delta sigma weight residual 123.10 116.84 6.26 9.60e-01 1.09e+00 4.25e+01 angle pdb=" N VAL A 219 " pdb=" CA VAL A 219 " pdb=" C VAL A 219 " ideal model delta sigma weight residual 108.35 100.25 8.10 1.32e+00 5.74e-01 3.77e+01 angle pdb=" C CYS B 114 " pdb=" N GLY B 115 " pdb=" CA GLY B 115 " ideal model delta sigma weight residual 121.61 125.52 -3.91 7.70e-01 1.69e+00 2.58e+01 angle pdb=" C VAL A 202 " pdb=" N GLY A 203 " pdb=" CA GLY A 203 " ideal model delta sigma weight residual 121.61 125.52 -3.91 7.70e-01 1.69e+00 2.58e+01 ... (remaining 13044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5284 17.91 - 35.83: 374 35.83 - 53.74: 75 53.74 - 71.66: 15 71.66 - 89.57: 2 Dihedral angle restraints: 5750 sinusoidal: 2236 harmonic: 3514 Sorted by residual: dihedral pdb=" CB CYS R 36 " pdb=" SG CYS R 36 " pdb=" SG CYS R 288 " pdb=" CB CYS R 288 " ideal model delta sinusoidal sigma weight residual -86.00 -175.57 89.57 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS C 7 " pdb=" SG CYS C 7 " pdb=" SG CYS C 48 " pdb=" CB CYS C 48 " ideal model delta sinusoidal sigma weight residual 93.00 150.18 -57.18 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA THR A 296 " pdb=" C THR A 296 " pdb=" N TYR A 297 " pdb=" CA TYR A 297 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 601 0.060 - 0.120: 607 0.120 - 0.179: 237 0.179 - 0.239: 44 0.239 - 0.299: 4 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA VAL A 219 " pdb=" N VAL A 219 " pdb=" C VAL A 219 " pdb=" CB VAL A 219 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA LEU C 15 " pdb=" N LEU C 15 " pdb=" C LEU C 15 " pdb=" CB LEU C 15 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1490 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 135 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO S 136 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO S 136 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO S 136 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 74 " -0.018 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C TYR R 74 " 0.066 2.00e-02 2.50e+03 pdb=" O TYR R 74 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS R 75 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 210 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C LYS A 210 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS A 210 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 211 " -0.013 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1551 2.83 - 3.35: 8695 3.35 - 3.87: 12654 3.87 - 4.38: 15974 4.38 - 4.90: 27265 Nonbonded interactions: 66139 Sorted by model distance: nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.318 2.520 nonbonded pdb=" O PHE R 71 " pdb=" NH2 ARG R 78 " model vdw 2.355 2.520 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.449 2.440 nonbonded pdb=" N VAL A 219 " pdb=" O VAL A 219 " model vdw 2.513 2.496 nonbonded pdb=" OG1 THR A 292 " pdb=" N GLY A 293 " model vdw 2.528 2.520 ... (remaining 66134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 5.740 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: 12.680 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.990 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.014 0.054 9641 Z= 0.927 Angle : 1.768 8.796 13049 Z= 1.321 Chirality : 0.091 0.299 1493 Planarity : 0.004 0.112 1644 Dihedral : 13.132 82.851 3462 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.10 % Allowed : 5.71 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.33 (0.19), residues: 1193 helix: -1.81 (0.21), residues: 368 sheet: -1.52 (0.30), residues: 235 loop : -2.78 (0.19), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS S 220 PHE 0.013 0.002 PHE Y 61 TYR 0.020 0.002 TYR R 125 ARG 0.004 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.997 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2342 time to fit residues: 56.8730 Evaluate side-chains 110 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 239 ASN C 3 ASN C 35 ASN A 205 GLN A 214 HIS A 305 GLN S 82 GLN S 174 GLN R 87 ASN R 128 ASN R 186 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9641 Z= 0.218 Angle : 0.619 9.160 13049 Z= 0.332 Chirality : 0.042 0.148 1493 Planarity : 0.004 0.061 1644 Dihedral : 5.047 62.366 1304 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.45 % Allowed : 11.33 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.44 (0.22), residues: 1193 helix: 0.91 (0.26), residues: 386 sheet: -1.16 (0.28), residues: 301 loop : -2.33 (0.22), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.002 PHE A 336 TYR 0.022 0.002 TYR R 296 ARG 0.004 0.001 ARG R 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.163 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 135 average time/residue: 0.2230 time to fit residues: 42.2513 Evaluate side-chains 109 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0802 time to fit residues: 2.5582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9641 Z= 0.189 Angle : 0.560 12.022 13049 Z= 0.291 Chirality : 0.041 0.138 1493 Planarity : 0.003 0.040 1644 Dihedral : 4.719 58.911 1304 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.55 % Allowed : 13.46 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1193 helix: 1.65 (0.26), residues: 385 sheet: -0.59 (0.29), residues: 293 loop : -2.26 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 292 TYR 0.015 0.001 TYR R 125 ARG 0.004 0.000 ARG S 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.033 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 126 average time/residue: 0.2028 time to fit residues: 36.3469 Evaluate side-chains 109 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0810 time to fit residues: 2.5627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.0010 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.0770 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 239 ASN C 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9641 Z= 0.118 Angle : 0.479 8.111 13049 Z= 0.251 Chirality : 0.039 0.129 1493 Planarity : 0.003 0.036 1644 Dihedral : 4.416 59.893 1304 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.94 % Allowed : 14.04 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.35 (0.23), residues: 1193 helix: 2.05 (0.26), residues: 385 sheet: -0.26 (0.30), residues: 294 loop : -2.09 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE B 292 TYR 0.013 0.001 TYR R 125 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.080 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 125 average time/residue: 0.2132 time to fit residues: 37.3771 Evaluate side-chains 111 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0852 time to fit residues: 3.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9641 Z= 0.162 Angle : 0.500 7.228 13049 Z= 0.262 Chirality : 0.040 0.134 1493 Planarity : 0.003 0.036 1644 Dihedral : 4.412 59.771 1304 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 15.68 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1193 helix: 2.20 (0.26), residues: 385 sheet: -0.07 (0.30), residues: 295 loop : -2.05 (0.22), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE B 292 TYR 0.014 0.001 TYR R 125 ARG 0.004 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.143 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 113 average time/residue: 0.2301 time to fit residues: 36.4824 Evaluate side-chains 104 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0858 time to fit residues: 2.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.5036 > 50: distance: 46 - 71: 10.738 distance: 50 - 80: 7.469 distance: 53 - 63: 13.023 distance: 54 - 85: 9.072 distance: 63 - 64: 7.870 distance: 64 - 65: 11.998 distance: 65 - 71: 14.939 distance: 66 - 94: 18.247 distance: 67 - 68: 16.340 distance: 67 - 69: 11.625 distance: 68 - 70: 13.546 distance: 71 - 72: 7.016 distance: 72 - 73: 10.975 distance: 72 - 75: 3.542 distance: 73 - 74: 10.111 distance: 73 - 80: 4.630 distance: 74 - 105: 23.351 distance: 75 - 76: 22.723 distance: 76 - 77: 8.205 distance: 77 - 78: 7.788 distance: 77 - 79: 26.254 distance: 80 - 81: 5.399 distance: 81 - 82: 7.439 distance: 81 - 84: 7.640 distance: 82 - 83: 18.031 distance: 82 - 85: 12.941 distance: 83 - 114: 31.778 distance: 85 - 86: 5.737 distance: 86 - 87: 7.934 distance: 86 - 89: 6.793 distance: 87 - 88: 14.551 distance: 87 - 94: 7.002 distance: 88 - 120: 26.580 distance: 89 - 90: 6.751 distance: 90 - 91: 7.883 distance: 91 - 92: 4.955 distance: 91 - 93: 17.616 distance: 94 - 95: 5.559 distance: 95 - 96: 4.904 distance: 95 - 98: 6.371 distance: 96 - 97: 22.433 distance: 96 - 105: 20.422 distance: 98 - 99: 6.740 distance: 99 - 100: 11.844 distance: 99 - 101: 8.244 distance: 100 - 102: 9.712 distance: 101 - 103: 5.759 distance: 102 - 104: 13.256 distance: 103 - 104: 10.266 distance: 105 - 106: 4.999 distance: 106 - 107: 10.452 distance: 106 - 109: 6.662 distance: 107 - 108: 9.090 distance: 107 - 114: 6.463 distance: 109 - 110: 12.420 distance: 110 - 111: 8.060 distance: 111 - 112: 4.588 distance: 111 - 113: 10.609 distance: 114 - 115: 6.013 distance: 115 - 116: 4.745 distance: 115 - 118: 13.694 distance: 116 - 117: 4.295 distance: 116 - 120: 7.179 distance: 118 - 119: 6.039 distance: 121 - 122: 13.850 distance: 121 - 124: 10.129 distance: 122 - 123: 18.417 distance: 122 - 129: 19.217 distance: 124 - 125: 14.100 distance: 125 - 126: 9.016 distance: 126 - 127: 39.715 distance: 127 - 128: 13.722 distance: 129 - 130: 15.367 distance: 130 - 131: 18.914 distance: 130 - 133: 13.585 distance: 131 - 132: 10.349 distance: 133 - 134: 11.102 distance: 134 - 135: 9.474 distance: 134 - 136: 22.185 distance: 137 - 138: 28.918 distance: 138 - 139: 6.700 distance: 138 - 141: 19.338 distance: 139 - 140: 21.511 distance: 139 - 148: 28.514 distance: 141 - 142: 15.767 distance: 142 - 143: 30.464 distance: 143 - 144: 6.976 distance: 144 - 145: 9.927 distance: 145 - 146: 11.255 distance: 145 - 147: 30.920