Starting phenix.real_space_refine on Sun Aug 4 10:10:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/08_2024/9auc_43877.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/08_2024/9auc_43877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/08_2024/9auc_43877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/08_2024/9auc_43877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/08_2024/9auc_43877.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/08_2024/9auc_43877.cif" } resolution = 2.4 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= 0.002 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 75 5.16 5 C 6629 2.51 5 N 1771 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R GLU 114": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10369 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1882 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 265 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "R" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3055 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 16, 'TRANS': 351} Chain: "P" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 184 Unusual residues: {'NAG': 3, 'PLM': 4, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 6.38, per 1000 atoms: 0.62 Number of scatterers: 10369 At special positions: 0 Unit cell: (97.5, 98.8, 163.15, 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 75 16.00 O 1894 8.00 N 1771 7.00 C 6629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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 Links applied NAG-ASN " NAG R 502 " - " ASN R 73 " " NAG R 503 " - " ASN R 125 " " NAG R 504 " - " ASN R 130 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 12 sheets defined 43.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.859A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.584A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.524A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.738A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.908A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.595A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.510A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.518A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.566A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.924A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.567A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.531A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 removed outlier: 4.274A pdb=" N CYS E 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 81 removed outlier: 4.091A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 78 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 120 through 143 Proline residue: E 126 - end of helix removed outlier: 3.516A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.937A pdb=" N LYS R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA R 51 " --> pdb=" O LYS R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 136 removed outlier: 3.536A pdb=" N ALA R 136 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.544A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.910A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 249 removed outlier: 3.637A pdb=" N HIS R 223 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 282 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 300 removed outlier: 3.920A pdb=" N LEU R 298 " --> pdb=" O THR R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 330 removed outlier: 3.502A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.589A pdb=" N PHE R 382 " --> pdb=" O SER R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 406 removed outlier: 3.578A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 6.274A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.613A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.556A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.556A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.544A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.854A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.765A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.661A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.504A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'R' and resid 93 through 94 476 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1678 1.32 - 1.45: 2966 1.45 - 1.57: 5843 1.57 - 1.69: 0 1.69 - 1.82: 106 Bond restraints: 10593 Sorted by residual: bond pdb=" N VAL R 147 " pdb=" CA VAL R 147 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.28e+00 bond pdb=" N ASP R 373 " pdb=" CA ASP R 373 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N LEU R 148 " pdb=" CA LEU R 148 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" CA ALA R 145 " pdb=" CB ALA R 145 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.83e+00 bond pdb=" N VAL R 375 " pdb=" CA VAL R 375 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.22e-02 6.72e+03 5.64e+00 ... (remaining 10588 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.24: 243 106.24 - 113.18: 5653 113.18 - 120.13: 3816 120.13 - 127.07: 4498 127.07 - 134.01: 133 Bond angle restraints: 14343 Sorted by residual: angle pdb=" C TYR R 150 " pdb=" CA TYR R 150 " pdb=" CB TYR R 150 " ideal model delta sigma weight residual 110.85 119.10 -8.25 1.70e+00 3.46e-01 2.36e+01 angle pdb=" C TYR R 374 " pdb=" CA TYR R 374 " pdb=" CB TYR R 374 " ideal model delta sigma weight residual 110.79 118.35 -7.56 1.66e+00 3.63e-01 2.07e+01 angle pdb=" CA ASP R 373 " pdb=" C ASP R 373 " pdb=" O ASP R 373 " ideal model delta sigma weight residual 120.82 116.46 4.36 1.05e+00 9.07e-01 1.72e+01 angle pdb=" C TYR R 146 " pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " ideal model delta sigma weight residual 110.85 117.30 -6.45 1.70e+00 3.46e-01 1.44e+01 angle pdb=" N ASP R 373 " pdb=" CA ASP R 373 " pdb=" C ASP R 373 " ideal model delta sigma weight residual 111.07 114.84 -3.77 1.07e+00 8.73e-01 1.24e+01 ... (remaining 14338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5966 17.92 - 35.84: 329 35.84 - 53.76: 96 53.76 - 71.67: 26 71.67 - 89.59: 19 Dihedral angle restraints: 6436 sinusoidal: 2723 harmonic: 3713 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -173.19 87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS E 27 " pdb=" SG CYS E 27 " pdb=" SG CYS E 82 " pdb=" CB CYS E 82 " ideal model delta sinusoidal sigma weight residual -86.00 -162.54 76.54 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 135.73 -42.73 1 1.00e+01 1.00e-02 2.55e+01 ... (remaining 6433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1478 0.076 - 0.151: 97 0.151 - 0.227: 5 0.227 - 0.302: 1 0.302 - 0.378: 2 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CA TYR R 150 " pdb=" N TYR R 150 " pdb=" C TYR R 150 " pdb=" CB TYR R 150 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA TYR R 146 " pdb=" N TYR R 146 " pdb=" C TYR R 146 " pdb=" CB TYR R 146 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA TYR R 374 " pdb=" N TYR R 374 " pdb=" C TYR R 374 " pdb=" CB TYR R 374 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1580 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 372 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C TYR R 372 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR R 372 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP R 373 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 141 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C LYS R 141 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS R 141 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 142 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.65e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1933 2.77 - 3.30: 9731 3.30 - 3.84: 17117 3.84 - 4.37: 20995 4.37 - 4.90: 35499 Nonbonded interactions: 85275 Sorted by model distance: nonbonded pdb=" O GLY E 52 " pdb=" NE1 TRP E 56 " model vdw 2.239 3.120 nonbonded pdb=" O SER A 306 " pdb=" OG SER A 306 " model vdw 2.314 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.317 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.320 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 3.040 ... (remaining 85270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.760 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.940 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.003 0.038 10593 Z= 0.172 Angle : 0.476 8.253 14343 Z= 0.287 Chirality : 0.042 0.378 1583 Planarity : 0.003 0.032 1809 Dihedral : 13.242 89.593 4010 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.91 % Allowed : 13.89 % Favored : 85.19 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.33 % 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: -3.20 (0.19), residues: 1256 helix: -2.79 (0.14), residues: 513 sheet: -1.02 (0.33), residues: 220 loop : -1.69 (0.23), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 56 HIS 0.002 0.000 HIS B 142 PHE 0.006 0.001 PHE E 101 TYR 0.018 0.001 TYR R 150 ARG 0.001 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8012 (mm110) cc_final: 0.7811 (pt0) REVERT: N 43 LYS cc_start: 0.7903 (mttp) cc_final: 0.7548 (mttm) REVERT: E 111 VAL cc_start: 0.7624 (t) cc_final: 0.7349 (p) REVERT: E 139 TRP cc_start: 0.7506 (t60) cc_final: 0.7246 (t60) REVERT: R 49 MET cc_start: 0.6247 (tpp) cc_final: 0.5393 (mtp) REVERT: R 120 LYS cc_start: 0.6372 (mttt) cc_final: 0.6120 (mmtt) REVERT: R 144 ASN cc_start: 0.7611 (m-40) cc_final: 0.7373 (m110) REVERT: R 215 ASP cc_start: 0.5995 (t0) cc_final: 0.5641 (m-30) REVERT: R 227 GLN cc_start: 0.7881 (mt0) cc_final: 0.7541 (mm110) REVERT: R 287 ASP cc_start: 0.6204 (t70) cc_final: 0.5792 (t70) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.4132 time to fit residues: 328.3656 Evaluate side-chains 135 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0030 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN A 254 ASN B 16 ASN B 75 GLN B 176 GLN B 266 HIS B 293 ASN N 1 GLN E 28 GLN E 45 GLN P 26 ASN R 61 GLN R 179 GLN R 223 HIS R 383 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10593 Z= 0.184 Angle : 0.515 9.123 14343 Z= 0.271 Chirality : 0.042 0.289 1583 Planarity : 0.004 0.037 1809 Dihedral : 5.465 59.713 1676 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.83 % Allowed : 18.56 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.87 (0.22), residues: 1256 helix: 0.07 (0.21), residues: 522 sheet: -0.49 (0.33), residues: 236 loop : -1.19 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.007 0.001 HIS R 381 PHE 0.013 0.001 PHE N 103 TYR 0.014 0.001 TYR R 191 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 1.141 Fit side-chains REVERT: N 87 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7359 (mttt) REVERT: E 76 MET cc_start: 0.3577 (ppp) cc_final: 0.3285 (ppp) REVERT: E 111 VAL cc_start: 0.7696 (t) cc_final: 0.7431 (p) REVERT: E 139 TRP cc_start: 0.7629 (t60) cc_final: 0.7395 (t60) REVERT: R 49 MET cc_start: 0.6319 (tpp) cc_final: 0.5451 (mtp) REVERT: R 120 LYS cc_start: 0.6451 (mttt) cc_final: 0.6221 (mmtt) REVERT: R 144 ASN cc_start: 0.7381 (m-40) cc_final: 0.7106 (m110) REVERT: R 146 TYR cc_start: 0.6923 (m-80) cc_final: 0.6705 (m-80) REVERT: R 174 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7081 (mtm-85) REVERT: R 215 ASP cc_start: 0.5934 (t0) cc_final: 0.5713 (t0) REVERT: R 227 GLN cc_start: 0.7823 (mt0) cc_final: 0.7399 (mm110) outliers start: 31 outliers final: 8 residues processed: 168 average time/residue: 1.4064 time to fit residues: 252.0726 Evaluate side-chains 134 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 174 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 1 GLN R 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10593 Z= 0.208 Angle : 0.529 9.350 14343 Z= 0.277 Chirality : 0.042 0.305 1583 Planarity : 0.004 0.045 1809 Dihedral : 5.566 59.525 1672 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.11 % Allowed : 18.65 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1256 helix: 1.02 (0.23), residues: 525 sheet: -0.39 (0.34), residues: 238 loop : -0.92 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 332 HIS 0.006 0.001 HIS R 277 PHE 0.016 0.002 PHE B 151 TYR 0.012 0.002 TYR N 80 ARG 0.005 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7990 (pt0) cc_final: 0.7755 (pt0) REVERT: B 75 GLN cc_start: 0.8694 (mm110) cc_final: 0.8425 (mm-40) REVERT: B 134 ARG cc_start: 0.7753 (ptp-110) cc_final: 0.7461 (ptm160) REVERT: N 87 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7347 (mttt) REVERT: E 49 GLU cc_start: 0.5194 (OUTLIER) cc_final: 0.4395 (tp30) REVERT: E 139 TRP cc_start: 0.7672 (t60) cc_final: 0.7376 (t60) REVERT: R 49 MET cc_start: 0.6350 (tpp) cc_final: 0.5498 (mtp) REVERT: R 120 LYS cc_start: 0.6608 (mttt) cc_final: 0.6362 (mmtt) REVERT: R 174 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7089 (mtm-85) REVERT: R 215 ASP cc_start: 0.5784 (t0) cc_final: 0.5572 (t0) REVERT: R 227 GLN cc_start: 0.7823 (mt0) cc_final: 0.7386 (mm110) REVERT: R 294 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: R 306 MET cc_start: 0.8544 (mmm) cc_final: 0.8294 (mmm) REVERT: R 403 LYS cc_start: 0.6494 (ptpp) cc_final: 0.6223 (mmmt) outliers start: 34 outliers final: 16 residues processed: 157 average time/residue: 1.4383 time to fit residues: 241.2064 Evaluate side-chains 139 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10593 Z= 0.192 Angle : 0.517 9.370 14343 Z= 0.270 Chirality : 0.042 0.302 1583 Planarity : 0.004 0.049 1809 Dihedral : 5.688 59.614 1672 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.83 % Allowed : 18.92 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1256 helix: 1.32 (0.23), residues: 526 sheet: -0.20 (0.34), residues: 226 loop : -0.76 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 236 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.011 0.001 TYR N 80 ARG 0.008 0.001 ARG R 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7941 (pt0) cc_final: 0.7690 (pt0) REVERT: A 368 ASP cc_start: 0.6851 (p0) cc_final: 0.6454 (p0) REVERT: B 195 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6431 (p0) REVERT: E 49 GLU cc_start: 0.5038 (OUTLIER) cc_final: 0.3951 (tp30) REVERT: E 111 VAL cc_start: 0.7795 (t) cc_final: 0.7531 (p) REVERT: E 139 TRP cc_start: 0.7649 (t60) cc_final: 0.7408 (t60) REVERT: R 49 MET cc_start: 0.6372 (tpp) cc_final: 0.5536 (mtp) REVERT: R 120 LYS cc_start: 0.6597 (mttt) cc_final: 0.6394 (mmmt) REVERT: R 174 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7091 (mtm-85) REVERT: R 227 GLN cc_start: 0.7812 (mt0) cc_final: 0.7395 (mm110) REVERT: R 288 ASN cc_start: 0.7100 (m-40) cc_final: 0.6833 (m-40) REVERT: R 306 MET cc_start: 0.8551 (mmm) cc_final: 0.8276 (mmm) REVERT: R 329 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: R 404 ARG cc_start: 0.7072 (ttp80) cc_final: 0.6780 (mtm-85) outliers start: 31 outliers final: 13 residues processed: 143 average time/residue: 1.3624 time to fit residues: 208.5301 Evaluate side-chains 141 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 329 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 120 GLN P 10 HIS R 121 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10593 Z= 0.261 Angle : 0.564 9.379 14343 Z= 0.296 Chirality : 0.044 0.320 1583 Planarity : 0.004 0.053 1809 Dihedral : 6.633 59.876 1672 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.38 % Allowed : 19.01 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1256 helix: 1.30 (0.23), residues: 528 sheet: -0.25 (0.33), residues: 233 loop : -0.77 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 76 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.013 0.002 TYR R 56 ARG 0.007 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7968 (pt0) cc_final: 0.7727 (pt0) REVERT: B 32 GLN cc_start: 0.6897 (mt0) cc_final: 0.6573 (mt0) REVERT: B 61 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8325 (ppp) REVERT: B 195 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6342 (p0) REVERT: B 197 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7276 (mmm160) REVERT: G 54 VAL cc_start: 0.4566 (OUTLIER) cc_final: 0.4333 (t) REVERT: E 49 GLU cc_start: 0.5075 (OUTLIER) cc_final: 0.3946 (tp30) REVERT: E 111 VAL cc_start: 0.7809 (t) cc_final: 0.7556 (p) REVERT: E 139 TRP cc_start: 0.7678 (t60) cc_final: 0.7444 (t60) REVERT: R 49 MET cc_start: 0.6382 (tpp) cc_final: 0.5540 (mtp) REVERT: R 120 LYS cc_start: 0.6635 (mttt) cc_final: 0.6425 (mmmt) REVERT: R 174 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7122 (mtm-85) REVERT: R 227 GLN cc_start: 0.7849 (mt0) cc_final: 0.7456 (mm110) REVERT: R 294 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7293 (mp0) outliers start: 37 outliers final: 13 residues processed: 148 average time/residue: 1.3500 time to fit residues: 213.6524 Evaluate side-chains 140 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10593 Z= 0.160 Angle : 0.494 9.444 14343 Z= 0.258 Chirality : 0.041 0.297 1583 Planarity : 0.003 0.052 1809 Dihedral : 6.257 59.682 1672 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.74 % Allowed : 20.02 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.57 (0.24), residues: 1256 helix: 1.65 (0.23), residues: 527 sheet: -0.20 (0.34), residues: 223 loop : -0.66 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.010 0.001 TYR N 80 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7908 (pt0) cc_final: 0.7696 (pt0) REVERT: B 195 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6426 (p0) REVERT: G 54 VAL cc_start: 0.4509 (OUTLIER) cc_final: 0.4298 (t) REVERT: E 49 GLU cc_start: 0.5097 (OUTLIER) cc_final: 0.3898 (tp30) REVERT: E 111 VAL cc_start: 0.7800 (t) cc_final: 0.7553 (p) REVERT: E 139 TRP cc_start: 0.7645 (t60) cc_final: 0.7383 (t60) REVERT: R 49 MET cc_start: 0.6319 (tpp) cc_final: 0.5489 (mtp) REVERT: R 120 LYS cc_start: 0.6593 (mttt) cc_final: 0.6378 (mmmt) REVERT: R 174 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7120 (mtm-85) REVERT: R 227 GLN cc_start: 0.7812 (mt0) cc_final: 0.7437 (mm110) outliers start: 30 outliers final: 11 residues processed: 144 average time/residue: 1.3232 time to fit residues: 203.6421 Evaluate side-chains 136 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10593 Z= 0.157 Angle : 0.499 9.204 14343 Z= 0.259 Chirality : 0.041 0.285 1583 Planarity : 0.003 0.052 1809 Dihedral : 6.150 59.312 1672 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 20.11 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.76 (0.24), residues: 1256 helix: 1.79 (0.23), residues: 528 sheet: -0.19 (0.34), residues: 234 loop : -0.49 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS R 381 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR N 80 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: B 61 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8289 (ppp) REVERT: B 195 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6430 (p0) REVERT: G 54 VAL cc_start: 0.4473 (OUTLIER) cc_final: 0.4254 (t) REVERT: N 87 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7406 (mttt) REVERT: E 49 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.3891 (tp30) REVERT: E 111 VAL cc_start: 0.7777 (t) cc_final: 0.7526 (p) REVERT: E 139 TRP cc_start: 0.7648 (t60) cc_final: 0.7385 (t60) REVERT: R 49 MET cc_start: 0.6270 (tpp) cc_final: 0.5445 (mtp) REVERT: R 120 LYS cc_start: 0.6605 (mttt) cc_final: 0.6391 (mmmt) REVERT: R 174 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7115 (mtm-85) REVERT: R 227 GLN cc_start: 0.7813 (mt0) cc_final: 0.7452 (mm110) outliers start: 31 outliers final: 12 residues processed: 142 average time/residue: 1.3727 time to fit residues: 208.6172 Evaluate side-chains 139 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 80 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10593 Z= 0.228 Angle : 0.548 9.416 14343 Z= 0.286 Chirality : 0.042 0.301 1583 Planarity : 0.004 0.054 1809 Dihedral : 6.770 59.996 1671 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.74 % Allowed : 20.57 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.66 (0.24), residues: 1256 helix: 1.68 (0.23), residues: 526 sheet: 0.01 (0.33), residues: 230 loop : -0.65 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 236 HIS 0.005 0.001 HIS B 62 PHE 0.017 0.002 PHE B 151 TYR 0.013 0.001 TYR A 311 ARG 0.007 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: B 9 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5955 (tm-30) REVERT: B 61 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8318 (ppp) REVERT: B 195 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6380 (p0) REVERT: G 54 VAL cc_start: 0.4557 (OUTLIER) cc_final: 0.4315 (t) REVERT: E 49 GLU cc_start: 0.5179 (OUTLIER) cc_final: 0.3889 (tp30) REVERT: E 111 VAL cc_start: 0.7787 (t) cc_final: 0.7554 (p) REVERT: E 139 TRP cc_start: 0.7645 (t60) cc_final: 0.7401 (t60) REVERT: R 49 MET cc_start: 0.6260 (tpp) cc_final: 0.5433 (mtp) REVERT: R 120 LYS cc_start: 0.6648 (mttt) cc_final: 0.6425 (mmmt) REVERT: R 174 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7108 (mtm-85) REVERT: R 227 GLN cc_start: 0.7852 (mt0) cc_final: 0.7466 (mm110) outliers start: 30 outliers final: 13 residues processed: 138 average time/residue: 1.3833 time to fit residues: 205.9700 Evaluate side-chains 132 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0070 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10593 Z= 0.207 Angle : 0.547 9.525 14343 Z= 0.285 Chirality : 0.042 0.302 1583 Planarity : 0.004 0.054 1809 Dihedral : 6.754 59.638 1671 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.56 % Allowed : 21.12 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.73 (0.24), residues: 1256 helix: 1.80 (0.23), residues: 520 sheet: -0.06 (0.33), residues: 232 loop : -0.60 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 76 HIS 0.004 0.001 HIS R 277 PHE 0.016 0.001 PHE B 151 TYR 0.012 0.001 TYR A 311 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6605 (mm-30) REVERT: B 61 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8303 (ppp) REVERT: B 195 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6410 (p0) REVERT: G 54 VAL cc_start: 0.4497 (OUTLIER) cc_final: 0.4277 (t) REVERT: E 49 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.3913 (tp30) REVERT: E 111 VAL cc_start: 0.7743 (t) cc_final: 0.7529 (p) REVERT: E 139 TRP cc_start: 0.7649 (t60) cc_final: 0.7411 (t60) REVERT: R 49 MET cc_start: 0.6241 (tpp) cc_final: 0.5416 (mtp) REVERT: R 120 LYS cc_start: 0.6634 (mttt) cc_final: 0.6434 (mmmt) REVERT: R 174 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7108 (mtm-85) REVERT: R 227 GLN cc_start: 0.7817 (mt0) cc_final: 0.7435 (mm110) outliers start: 28 outliers final: 12 residues processed: 132 average time/residue: 1.3154 time to fit residues: 185.9036 Evaluate side-chains 133 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10593 Z= 0.292 Angle : 0.610 9.633 14343 Z= 0.318 Chirality : 0.045 0.307 1583 Planarity : 0.004 0.055 1809 Dihedral : 7.179 59.942 1671 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.10 % Allowed : 21.85 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1256 helix: 1.59 (0.23), residues: 521 sheet: -0.03 (0.32), residues: 231 loop : -0.69 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 76 HIS 0.005 0.001 HIS B 62 PHE 0.018 0.002 PHE B 151 TYR 0.016 0.002 TYR A 311 ARG 0.008 0.001 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.7000 (mtm-85) REVERT: B 61 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8325 (ppp) REVERT: B 195 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6370 (p0) REVERT: G 54 VAL cc_start: 0.4560 (OUTLIER) cc_final: 0.4323 (t) REVERT: E 49 GLU cc_start: 0.5252 (OUTLIER) cc_final: 0.3935 (tp30) REVERT: E 139 TRP cc_start: 0.7647 (t60) cc_final: 0.7444 (t60) REVERT: R 49 MET cc_start: 0.6237 (tpp) cc_final: 0.5398 (mtp) REVERT: R 174 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7095 (mtm-85) REVERT: R 227 GLN cc_start: 0.7853 (mt0) cc_final: 0.7472 (mm110) outliers start: 23 outliers final: 11 residues processed: 129 average time/residue: 1.2954 time to fit residues: 179.6100 Evaluate side-chains 128 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 14 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 1 GLN N 120 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.179925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125058 restraints weight = 12924.882| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.87 r_work: 0.3432 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10593 Z= 0.160 Angle : 0.527 9.410 14343 Z= 0.274 Chirality : 0.041 0.290 1583 Planarity : 0.004 0.060 1809 Dihedral : 6.416 59.916 1671 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.46 % Allowed : 22.49 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.89 (0.24), residues: 1256 helix: 1.95 (0.23), residues: 522 sheet: -0.03 (0.33), residues: 236 loop : -0.52 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 76 HIS 0.003 0.001 HIS R 277 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR R 146 ARG 0.016 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4900.69 seconds wall clock time: 86 minutes 2.78 seconds (5162.78 seconds total)