Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 18:33:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu9_32824/04_2023/7wu9_32824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu9_32824/04_2023/7wu9_32824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.375 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu9_32824/04_2023/7wu9_32824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu9_32824/04_2023/7wu9_32824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu9_32824/04_2023/7wu9_32824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu9_32824/04_2023/7wu9_32824.pdb" } resolution = 3.375 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Anisotropic ADP refinement not supported. Converting 780 atoms to isotropic. 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 47 5.16 5 C 4645 2.51 5 N 1279 2.21 5 O 1398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7369 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1758 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 1753 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 265} Chain breaks: 5 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 180 Conformer: "B" Number of residues, atoms: 274, 1753 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 265} Chain breaks: 5 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 12, 'GLU:plan': 2, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 180 bond proxies already assigned to first conformer: 1776 Chain: "A" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1018 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 134} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2487 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Chain: "G" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 345 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "S" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE R 236 " occ=0.50 ... (8 atoms not shown) pdb=" CB BPHE R 236 " occ=0.50 Time building chain proxies: 5.19, per 1000 atoms: 0.70 Number of scatterers: 7369 At special positions: 0 Unit cell: (116.1, 118.8, 95.175, 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 47 16.00 O 1398 8.00 N 1279 7.00 C 4645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 130 " - pdb=" SG CYS R 208 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 38.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'R' and resid 52 through 75 removed outlier: 4.254A pdb=" N ILE R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 116 removed outlier: 3.613A pdb=" N LEU R 89 " --> pdb=" O LYS R 85 " (cutoff:3.500A) Proline residue: R 108 - end of helix Processing helix chain 'R' and resid 127 through 161 removed outlier: 3.532A pdb=" N LEU R 145 " --> pdb=" O GLY R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 169 removed outlier: 3.790A pdb=" N ALA R 166 " --> pdb=" O PRO R 162 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER R 167 " --> pdb=" O HIS R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 195 removed outlier: 3.574A pdb=" N ARG R 175 " --> pdb=" O THR R 171 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL R 181 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP R 182 " --> pdb=" O LEU R 178 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 183 " --> pdb=" O LEU R 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU R 191 " --> pdb=" O ALA R 187 " (cutoff:3.500A) Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 227 through 265 removed outlier: 3.561A pdb=" N ALA R 231 " --> pdb=" O ASN R 227 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 308 removed outlier: 3.711A pdb=" N ILE R 276 " --> pdb=" O GLN R 272 " (cutoff:3.500A) Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 324 through 347 removed outlier: 4.087A pdb=" N PHE R 328 " --> pdb=" O GLU R 324 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN R 338 " --> pdb=" O LEU R 334 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 3.799A pdb=" N TYR R 346 " --> pdb=" O ASP R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 357 removed outlier: 3.898A pdb=" N LYS R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE R 352 " --> pdb=" O LEU R 348 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE R 357 " --> pdb=" O LEU R 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.861A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.858A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.776A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.923A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.729A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.854A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 10 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.524A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.503A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.604A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'R' and resid 199 through 201 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.801A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 52 removed outlier: 4.079A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.510A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.519A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.841A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.054A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.463A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.084A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.544A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.521A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 148 removed outlier: 6.101A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 148 removed outlier: 6.101A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN S 231 " --> pdb=" O THR S 238 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1087 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: 2.33 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2437 1.34 - 1.46: 1815 1.46 - 1.58: 3192 1.58 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 7509 Sorted by residual: bond pdb=" CA HIS A 195 " pdb=" C HIS A 195 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 5.32e-01 bond pdb=" CG ARG R 350 " pdb=" CD ARG R 350 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.76e-01 bond pdb=" CB PRO S 236 " pdb=" CG PRO S 236 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.25e-01 bond pdb=" CB LYS A 29 " pdb=" CG LYS A 29 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.22e-01 bond pdb=" CB ARG R 350 " pdb=" CG ARG R 350 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.10e-01 ... (remaining 7504 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 170 107.08 - 113.80: 4261 113.80 - 120.53: 2806 120.53 - 127.25: 2919 127.25 - 133.98: 84 Bond angle restraints: 10240 Sorted by residual: angle pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" O HIS A 195 " ideal model delta sigma weight residual 122.64 120.41 2.23 1.25e+00 6.40e-01 3.19e+00 angle pdb=" CA TYR S 190 " pdb=" CB TYR S 190 " pdb=" CG TYR S 190 " ideal model delta sigma weight residual 113.90 117.01 -3.11 1.80e+00 3.09e-01 2.99e+00 angle pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N PHE A 196 " ideal model delta sigma weight residual 114.76 116.67 -1.91 1.14e+00 7.69e-01 2.81e+00 angle pdb=" CA GLN S 13 " pdb=" CB GLN S 13 " pdb=" CG GLN S 13 " ideal model delta sigma weight residual 114.10 117.43 -3.33 2.00e+00 2.50e-01 2.78e+00 angle pdb=" CB ARG R 350 " pdb=" CG ARG R 350 " pdb=" CD ARG R 350 " ideal model delta sigma weight residual 111.30 115.03 -3.73 2.30e+00 1.89e-01 2.62e+00 ... (remaining 10235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4014 17.97 - 35.94: 292 35.94 - 53.91: 56 53.91 - 71.88: 4 71.88 - 89.85: 5 Dihedral angle restraints: 4371 sinusoidal: 1406 harmonic: 2965 Sorted by residual: dihedral pdb=" CB CYS R 130 " pdb=" SG CYS R 130 " pdb=" SG CYS R 208 " pdb=" CB CYS R 208 " ideal model delta sinusoidal sigma weight residual -86.00 -156.77 70.77 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA THR B 179 " pdb=" C THR B 179 " pdb=" N PHE B 180 " pdb=" CA PHE B 180 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 786 0.029 - 0.058: 288 0.058 - 0.087: 69 0.087 - 0.116: 51 0.116 - 0.145: 20 Chirality restraints: 1214 Sorted by residual: chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1211 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO G 49 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 236 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.010 2.00e-02 2.50e+03 8.76e-03 1.34e+00 pdb=" CG PHE B 234 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 199 2.69 - 3.24: 7472 3.24 - 3.79: 11242 3.79 - 4.35: 14713 4.35 - 4.90: 24981 Nonbonded interactions: 58607 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.137 2.440 nonbonded pdb=" O ASP A 337 " pdb=" OG1 THR A 340 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR S 101 " pdb=" NE2 HIS S 232 " model vdw 2.227 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.229 2.440 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.248 2.440 ... (remaining 58602 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=0.50 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 9.640 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 7509 Z= 0.160 Angle : 0.424 4.615 10240 Z= 0.227 Chirality : 0.039 0.145 1214 Planarity : 0.002 0.032 1309 Dihedral : 13.281 89.849 2448 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.21 (0.28), residues: 1003 helix: 3.10 (0.28), residues: 341 sheet: -0.68 (0.30), residues: 303 loop : -0.02 (0.33), residues: 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2617 time to fit residues: 58.5331 Evaluate side-chains 140 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN G 59 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7509 Z= 0.177 Angle : 0.570 10.372 10240 Z= 0.293 Chirality : 0.043 0.152 1214 Planarity : 0.003 0.037 1309 Dihedral : 3.716 24.440 1085 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.10 (0.27), residues: 1003 helix: 2.67 (0.27), residues: 344 sheet: -0.30 (0.31), residues: 293 loop : -0.17 (0.33), residues: 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 0.887 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 165 average time/residue: 0.2420 time to fit residues: 50.7290 Evaluate side-chains 152 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0670 time to fit residues: 1.9669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7509 Z= 0.252 Angle : 0.563 10.631 10240 Z= 0.290 Chirality : 0.043 0.161 1214 Planarity : 0.003 0.040 1309 Dihedral : 3.764 27.229 1085 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.03 (0.27), residues: 1003 helix: 2.58 (0.27), residues: 345 sheet: -0.29 (0.30), residues: 298 loop : -0.23 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.761 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 148 average time/residue: 0.2471 time to fit residues: 46.9274 Evaluate side-chains 140 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0844 time to fit residues: 1.6225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7509 Z= 0.175 Angle : 0.536 9.622 10240 Z= 0.275 Chirality : 0.042 0.151 1214 Planarity : 0.003 0.038 1309 Dihedral : 3.582 19.172 1085 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.09 (0.27), residues: 1003 helix: 2.56 (0.28), residues: 343 sheet: -0.17 (0.30), residues: 295 loop : -0.21 (0.33), residues: 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.075 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 144 average time/residue: 0.2489 time to fit residues: 45.5100 Evaluate side-chains 147 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0710 time to fit residues: 1.8366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 0.0050 chunk 40 optimal weight: 0.0070 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.0670 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.1950 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7509 Z= 0.142 Angle : 0.515 10.116 10240 Z= 0.262 Chirality : 0.042 0.156 1214 Planarity : 0.003 0.038 1309 Dihedral : 3.412 15.612 1085 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.15 (0.27), residues: 1003 helix: 2.61 (0.28), residues: 343 sheet: -0.14 (0.30), residues: 300 loop : -0.16 (0.34), residues: 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.835 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 154 average time/residue: 0.2558 time to fit residues: 50.6568 Evaluate side-chains 142 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0768 time to fit residues: 1.6661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7509 Z= 0.291 Angle : 0.570 9.764 10240 Z= 0.294 Chirality : 0.043 0.165 1214 Planarity : 0.003 0.040 1309 Dihedral : 3.701 15.918 1085 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.19 (0.27), residues: 1003 helix: 2.69 (0.28), residues: 343 sheet: -0.13 (0.30), residues: 297 loop : -0.19 (0.33), residues: 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.886 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 150 average time/residue: 0.2357 time to fit residues: 45.5492 Evaluate side-chains 149 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0762 time to fit residues: 2.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7509 Z= 0.224 Angle : 0.554 11.061 10240 Z= 0.285 Chirality : 0.043 0.188 1214 Planarity : 0.003 0.039 1309 Dihedral : 3.672 16.252 1085 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.17 (0.27), residues: 1003 helix: 2.69 (0.28), residues: 343 sheet: -0.17 (0.29), residues: 297 loop : -0.17 (0.33), residues: 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.878 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 142 average time/residue: 0.2444 time to fit residues: 44.4897 Evaluate side-chains 144 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1550 time to fit residues: 2.2513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7509 Z= 0.312 Angle : 0.590 10.699 10240 Z= 0.304 Chirality : 0.044 0.206 1214 Planarity : 0.003 0.040 1309 Dihedral : 3.839 16.161 1085 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.09 (0.27), residues: 1003 helix: 2.68 (0.28), residues: 343 sheet: -0.25 (0.29), residues: 297 loop : -0.25 (0.33), residues: 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.924 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 149 average time/residue: 0.2395 time to fit residues: 45.9683 Evaluate side-chains 143 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0810 time to fit residues: 1.7141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7509 Z= 0.200 Angle : 0.578 11.604 10240 Z= 0.293 Chirality : 0.043 0.231 1214 Planarity : 0.003 0.040 1309 Dihedral : 3.666 16.417 1085 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.16 (0.27), residues: 1003 helix: 2.73 (0.28), residues: 338 sheet: -0.22 (0.29), residues: 297 loop : -0.16 (0.33), residues: 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 0.827 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2338 time to fit residues: 44.1155 Evaluate side-chains 138 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7509 Z= 0.223 Angle : 0.581 11.135 10240 Z= 0.298 Chirality : 0.043 0.238 1214 Planarity : 0.003 0.041 1309 Dihedral : 3.669 17.005 1085 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.17 (0.27), residues: 1003 helix: 2.73 (0.28), residues: 338 sheet: -0.21 (0.30), residues: 297 loop : -0.15 (0.33), residues: 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2006 Ramachandran restraints generated. 1003 Oldfield, 0 Emsley, 1003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.865 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 142 average time/residue: 0.2373 time to fit residues: 43.6618 Evaluate side-chains 147 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0837 time to fit residues: 1.4408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 40.0000 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.185144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111414 restraints weight = 9512.414| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.01 r_work: 0.3050 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7509 Z= 0.209 Angle : 0.587 10.775 10240 Z= 0.298 Chirality : 0.043 0.238 1214 Planarity : 0.003 0.040 1309 Dihedral : 3.625 17.281 1085 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.17 (0.27), residues: 1003 helix: 2.72 (0.28), residues: 338 sheet: -0.24 (0.29), residues: 297 loop : -0.11 (0.34), residues: 368 =============================================================================== Job complete usr+sys time: 2110.26 seconds wall clock time: 38 minutes 42.56 seconds (2322.56 seconds total)