Starting phenix.real_space_refine on Sat Jul 20 07:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/07_2024/9auc_43877.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/07_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_43877/07_2024/9auc_43877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/07_2024/9auc_43877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/07_2024/9auc_43877.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9auc_43877/07_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.34, per 1000 atoms: 0.71 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: 4.15 Conformation dependent library (CDL) restraints added in 2.0 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: 1.39 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: 3.16 Time building geometry restraints manager: 4.53 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 2.520 nonbonded pdb=" O SER A 306 " pdb=" OG SER A 306 " model vdw 2.314 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.317 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.320 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 2.440 ... (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 ========== 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: 11.950 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.210 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.630 ------------------------------------------------------------------------------- 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 : 1.178 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: 1.4109 time to fit residues: 327.1270 Evaluate side-chains 135 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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: 0.0770 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 B 16 ASN 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 226 HIS R 383 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10593 Z= 0.275 Angle : 0.577 9.378 14343 Z= 0.304 Chirality : 0.044 0.298 1583 Planarity : 0.005 0.043 1809 Dihedral : 6.067 58.626 1676 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.75 % Allowed : 18.19 % Favored : 78.06 % 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: -0.88 (0.22), residues: 1256 helix: 0.03 (0.21), residues: 524 sheet: -0.48 (0.33), residues: 241 loop : -1.16 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.008 0.002 HIS R 277 PHE 0.019 0.002 PHE R 253 TYR 0.014 0.002 TYR R 191 ARG 0.007 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 182 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.027 Fit side-chains REVERT: A 35 GLN cc_start: 0.7913 (mm110) cc_final: 0.7699 (pt0) REVERT: B 195 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6372 (p0) REVERT: B 214 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7664 (mpt180) REVERT: N 87 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7378 (mttt) REVERT: E 76 MET cc_start: 0.3625 (ppp) cc_final: 0.3346 (ppp) REVERT: E 111 VAL cc_start: 0.7674 (t) cc_final: 0.7427 (p) REVERT: E 139 TRP cc_start: 0.7678 (t60) cc_final: 0.7410 (t60) REVERT: R 49 MET cc_start: 0.6331 (tpp) cc_final: 0.5394 (mtp) REVERT: R 120 LYS cc_start: 0.6512 (mttt) cc_final: 0.6273 (mmtt) REVERT: R 144 ASN cc_start: 0.7435 (m-40) cc_final: 0.7217 (m-40) REVERT: R 174 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7106 (mtm-85) REVERT: R 215 ASP cc_start: 0.5974 (t0) cc_final: 0.5329 (m-30) REVERT: R 227 GLN cc_start: 0.7858 (mt0) cc_final: 0.7425 (mm110) REVERT: R 294 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: R 403 LYS cc_start: 0.6454 (ptpp) cc_final: 0.6125 (mmmt) outliers start: 41 outliers final: 14 residues processed: 172 average time/residue: 1.3502 time to fit residues: 247.5907 Evaluate side-chains 139 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 136 SER 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 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 78 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 294 GLU 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: 1.9990 chunk 92 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 R 121 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10593 Z= 0.260 Angle : 0.565 9.170 14343 Z= 0.297 Chirality : 0.044 0.289 1583 Planarity : 0.004 0.057 1809 Dihedral : 6.325 59.854 1672 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.11 % Allowed : 17.64 % 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: -0.09 (0.23), residues: 1256 helix: 0.89 (0.23), residues: 528 sheet: -0.31 (0.33), residues: 241 loop : -0.88 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 332 HIS 0.006 0.002 HIS A 357 PHE 0.020 0.002 PHE B 151 TYR 0.011 0.002 TYR R 391 ARG 0.006 0.001 ARG A 347 *********************** 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 175 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 130 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 368 ASP cc_start: 0.6994 (p0) cc_final: 0.6605 (p0) REVERT: B 32 GLN cc_start: 0.7052 (mt0) cc_final: 0.6688 (mt0) REVERT: E 111 VAL cc_start: 0.7675 (t) cc_final: 0.7439 (p) REVERT: E 139 TRP cc_start: 0.7689 (t60) cc_final: 0.7444 (t60) REVERT: R 49 MET cc_start: 0.6374 (tpp) cc_final: 0.5471 (mtp) REVERT: R 120 LYS cc_start: 0.6619 (mttt) cc_final: 0.6368 (mmtt) REVERT: R 144 ASN cc_start: 0.7441 (m-40) cc_final: 0.7235 (m-40) REVERT: R 174 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7078 (mtm-85) REVERT: R 227 GLN cc_start: 0.7835 (mt0) cc_final: 0.7403 (mm110) REVERT: R 294 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: R 306 MET cc_start: 0.8617 (mmm) cc_final: 0.8254 (mmm) REVERT: R 404 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6774 (mtm-85) outliers start: 45 outliers final: 16 residues processed: 162 average time/residue: 1.2968 time to fit residues: 225.4379 Evaluate side-chains 138 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 249 THR 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 78 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN N 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10593 Z= 0.195 Angle : 0.512 9.397 14343 Z= 0.266 Chirality : 0.041 0.285 1583 Planarity : 0.003 0.056 1809 Dihedral : 6.180 59.996 1672 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.66 % Allowed : 18.74 % 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: 0.30 (0.24), residues: 1256 helix: 1.32 (0.23), residues: 528 sheet: -0.10 (0.33), residues: 229 loop : -0.81 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE B 151 TYR 0.010 0.001 TYR R 149 ARG 0.007 0.000 ARG B 214 *********************** 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 163 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7977 (pt0) cc_final: 0.7728 (pt0) REVERT: B 195 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6381 (p0) REVERT: B 214 ARG cc_start: 0.7947 (mpt-90) cc_final: 0.7619 (mpt180) REVERT: E 49 GLU cc_start: 0.4787 (OUTLIER) cc_final: 0.3643 (tp30) REVERT: E 111 VAL cc_start: 0.7692 (t) cc_final: 0.7475 (p) REVERT: E 139 TRP cc_start: 0.7682 (t60) cc_final: 0.7425 (t60) REVERT: R 49 MET cc_start: 0.6385 (tpp) cc_final: 0.5516 (mtp) REVERT: R 120 LYS cc_start: 0.6620 (mttt) cc_final: 0.6369 (mmtt) REVERT: R 144 ASN cc_start: 0.7417 (m-40) cc_final: 0.7213 (m-40) REVERT: R 150 TYR cc_start: 0.6996 (m-10) cc_final: 0.6594 (m-80) REVERT: R 174 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7030 (mtm-85) REVERT: R 227 GLN cc_start: 0.7827 (mt0) cc_final: 0.7421 (mm110) REVERT: R 294 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: R 306 MET cc_start: 0.8607 (mmm) cc_final: 0.8248 (mmm) REVERT: R 404 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6760 (mtm-85) outliers start: 40 outliers final: 16 residues processed: 146 average time/residue: 1.3615 time to fit residues: 212.6578 Evaluate side-chains 138 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 325 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 78 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR 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 274 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 77 ASN P 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10593 Z= 0.193 Angle : 0.507 9.490 14343 Z= 0.263 Chirality : 0.041 0.286 1583 Planarity : 0.003 0.058 1809 Dihedral : 6.463 59.674 1672 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.38 % Allowed : 19.38 % 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: 0.53 (0.24), residues: 1256 helix: 1.53 (0.23), residues: 529 sheet: 0.02 (0.33), residues: 227 loop : -0.73 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.010 0.001 TYR A 311 ARG 0.008 0.000 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 163 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7968 (pt0) cc_final: 0.7726 (pt0) REVERT: B 9 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.5916 (tm-30) REVERT: B 195 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6434 (p0) REVERT: B 214 ARG cc_start: 0.7946 (mpt-90) cc_final: 0.7607 (mpt180) REVERT: G 54 VAL cc_start: 0.4534 (OUTLIER) cc_final: 0.4307 (t) REVERT: E 49 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.3691 (tp30) REVERT: E 139 TRP cc_start: 0.7660 (t60) cc_final: 0.7434 (t60) REVERT: R 49 MET cc_start: 0.6306 (tpp) cc_final: 0.5477 (mtp) REVERT: R 120 LYS cc_start: 0.6630 (mttt) cc_final: 0.6382 (mmtt) REVERT: R 150 TYR cc_start: 0.6942 (m-10) cc_final: 0.6511 (m-80) REVERT: R 174 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7068 (mtm-85) REVERT: R 227 GLN cc_start: 0.7812 (mt0) cc_final: 0.7420 (mm110) REVERT: R 294 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: R 306 MET cc_start: 0.8626 (mmm) cc_final: 0.8315 (mmm) outliers start: 37 outliers final: 16 residues processed: 149 average time/residue: 1.2397 time to fit residues: 198.5989 Evaluate side-chains 143 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 249 THR 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 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR 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 274 THR 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: 0.6980 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN P 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10593 Z= 0.133 Angle : 0.467 9.436 14343 Z= 0.241 Chirality : 0.040 0.271 1583 Planarity : 0.003 0.056 1809 Dihedral : 6.077 59.792 1672 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.65 % Allowed : 20.48 % Favored : 76.87 % 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: 0.88 (0.24), residues: 1256 helix: 1.87 (0.24), residues: 529 sheet: 0.19 (0.34), residues: 234 loop : -0.60 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS R 381 PHE 0.013 0.001 PHE B 151 TYR 0.008 0.001 TYR N 60 ARG 0.005 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 153 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7931 (pt0) cc_final: 0.7707 (pt0) REVERT: A 368 ASP cc_start: 0.6741 (p0) cc_final: 0.6266 (p0) REVERT: B 195 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6498 (p0) REVERT: B 214 ARG cc_start: 0.7911 (mpt-90) cc_final: 0.7568 (mpt180) REVERT: G 54 VAL cc_start: 0.4415 (OUTLIER) cc_final: 0.4177 (t) REVERT: E 49 GLU cc_start: 0.4893 (OUTLIER) cc_final: 0.3601 (tp30) REVERT: E 139 TRP cc_start: 0.7653 (t60) cc_final: 0.7426 (t60) REVERT: R 49 MET cc_start: 0.6230 (tpp) cc_final: 0.5451 (mtp) REVERT: R 120 LYS cc_start: 0.6628 (mttt) cc_final: 0.6414 (mmmt) REVERT: R 150 TYR cc_start: 0.6950 (m-10) cc_final: 0.6688 (m-10) REVERT: R 227 GLN cc_start: 0.7799 (mt0) cc_final: 0.7441 (mm110) REVERT: R 306 MET cc_start: 0.8581 (mmm) cc_final: 0.8198 (mmm) outliers start: 29 outliers final: 13 residues processed: 143 average time/residue: 1.3231 time to fit residues: 202.6024 Evaluate side-chains 134 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 195 ASP 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 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 274 THR 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: 0.4980 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 118 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.6122 ------------------------------------------------------------------------------- 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 E 43 GLN P 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3975 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= 0.220 Angle : 0.538 9.309 14343 Z= 0.277 Chirality : 0.042 0.288 1583 Planarity : 0.004 0.057 1809 Dihedral : 6.662 59.808 1671 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.02 % Allowed : 20.38 % Favored : 76.60 % 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: 0.82 (0.24), residues: 1256 helix: 1.82 (0.23), residues: 526 sheet: 0.24 (0.33), residues: 231 loop : -0.66 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 236 HIS 0.005 0.001 HIS R 277 PHE 0.017 0.002 PHE B 151 TYR 0.015 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 159 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7938 (pt0) cc_final: 0.7694 (pt0) REVERT: A 327 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: B 195 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6421 (p0) REVERT: B 214 ARG cc_start: 0.7929 (mpt-90) cc_final: 0.7599 (mpt180) REVERT: G 54 VAL cc_start: 0.4620 (OUTLIER) cc_final: 0.4368 (t) REVERT: E 49 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.4047 (tp30) REVERT: E 139 TRP cc_start: 0.7660 (t60) cc_final: 0.7456 (t60) REVERT: R 49 MET cc_start: 0.6250 (tpp) cc_final: 0.5464 (mtp) REVERT: R 120 LYS cc_start: 0.6612 (mttt) cc_final: 0.6380 (mmtt) REVERT: R 150 TYR cc_start: 0.6927 (m-10) cc_final: 0.6670 (m-10) REVERT: R 227 GLN cc_start: 0.7842 (mt0) cc_final: 0.7462 (mm110) REVERT: R 229 MET cc_start: 0.8786 (tpp) cc_final: 0.8521 (tpp) REVERT: R 294 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: R 306 MET cc_start: 0.8650 (mmm) cc_final: 0.8327 (mmm) outliers start: 33 outliers final: 18 residues processed: 144 average time/residue: 1.3301 time to fit residues: 205.1022 Evaluate side-chains 146 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 172 GLU 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 B residue 325 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 54 VAL 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 199 ILE Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10593 Z= 0.258 Angle : 0.565 9.401 14343 Z= 0.294 Chirality : 0.043 0.313 1583 Planarity : 0.004 0.060 1809 Dihedral : 7.025 59.228 1671 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.11 % Allowed : 20.75 % Favored : 76.14 % 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: 1.74 (0.23), residues: 523 sheet: 0.13 (0.33), residues: 234 loop : -0.66 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 236 HIS 0.005 0.001 HIS B 62 PHE 0.018 0.002 PHE B 151 TYR 0.013 0.002 TYR A 311 ARG 0.005 0.001 ARG A 265 *********************** 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 158 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7926 (pt0) cc_final: 0.7719 (pt0) REVERT: B 9 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5993 (tm-30) REVERT: B 32 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6589 (mt0) REVERT: B 195 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6392 (p0) REVERT: B 214 ARG cc_start: 0.7917 (mpt-90) cc_final: 0.7598 (mpt180) REVERT: G 54 VAL cc_start: 0.4646 (OUTLIER) cc_final: 0.4402 (t) REVERT: E 48 MET cc_start: 0.0222 (ttt) cc_final: -0.0062 (ttm) REVERT: E 49 GLU cc_start: 0.5282 (OUTLIER) cc_final: 0.4255 (tp30) REVERT: R 49 MET cc_start: 0.6287 (tpp) cc_final: 0.5480 (mtp) REVERT: R 120 LYS cc_start: 0.6627 (mttt) cc_final: 0.6403 (mmtt) REVERT: R 150 TYR cc_start: 0.6926 (m-10) cc_final: 0.6689 (m-10) REVERT: R 227 GLN cc_start: 0.7842 (mt0) cc_final: 0.7462 (mm110) REVERT: R 294 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: R 306 MET cc_start: 0.8634 (mmm) cc_final: 0.8306 (mmm) REVERT: R 403 LYS cc_start: 0.6276 (OUTLIER) cc_final: 0.6014 (mtpp) outliers start: 34 outliers final: 15 residues processed: 146 average time/residue: 1.3994 time to fit residues: 220.1907 Evaluate side-chains 143 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 65 THR 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 54 VAL Chi-restraints excluded: chain N residue 12 VAL 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 199 ILE Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 403 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0870 chunk 110 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10593 Z= 0.133 Angle : 0.478 9.370 14343 Z= 0.247 Chirality : 0.040 0.283 1583 Planarity : 0.003 0.059 1809 Dihedral : 6.310 59.196 1671 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.37 % Allowed : 22.94 % Favored : 75.69 % 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: 1.09 (0.24), residues: 1256 helix: 2.11 (0.24), residues: 521 sheet: 0.14 (0.33), residues: 250 loop : -0.44 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS R 381 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR N 80 ARG 0.005 0.000 ARG A 265 *********************** 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 140 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: B 214 ARG cc_start: 0.7918 (mpt-90) cc_final: 0.7570 (mpt180) REVERT: G 54 VAL cc_start: 0.4500 (OUTLIER) cc_final: 0.4259 (t) REVERT: E 48 MET cc_start: 0.0601 (ttt) cc_final: 0.0307 (ttm) REVERT: E 49 GLU cc_start: 0.5187 (OUTLIER) cc_final: 0.4080 (tp30) REVERT: R 49 MET cc_start: 0.6212 (tpp) cc_final: 0.5447 (mtp) REVERT: R 227 GLN cc_start: 0.7778 (mt0) cc_final: 0.7431 (mm110) REVERT: R 294 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: R 306 MET cc_start: 0.8577 (mmm) cc_final: 0.8196 (mmm) outliers start: 15 outliers final: 8 residues processed: 133 average time/residue: 1.3566 time to fit residues: 193.1753 Evaluate side-chains 133 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 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 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: 0.8086 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10593 Z= 0.174 Angle : 0.507 9.405 14343 Z= 0.261 Chirality : 0.041 0.290 1583 Planarity : 0.003 0.059 1809 Dihedral : 6.387 59.607 1671 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 22.94 % Favored : 75.69 % 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: 1.09 (0.24), residues: 1256 helix: 2.12 (0.23), residues: 519 sheet: 0.31 (0.34), residues: 237 loop : -0.54 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 139 HIS 0.004 0.001 HIS R 381 PHE 0.015 0.001 PHE B 151 TYR 0.013 0.001 TYR R 146 ARG 0.007 0.000 ARG A 265 ********************** 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 137 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 327 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6626 (mm-30) REVERT: B 214 ARG cc_start: 0.7886 (mpt-90) cc_final: 0.7588 (mpt180) REVERT: G 54 VAL cc_start: 0.4510 (OUTLIER) cc_final: 0.4264 (t) REVERT: N 87 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7314 (mttt) REVERT: E 49 GLU cc_start: 0.5040 (OUTLIER) cc_final: 0.3978 (tp30) REVERT: R 49 MET cc_start: 0.6189 (tpp) cc_final: 0.5473 (mtp) REVERT: R 227 GLN cc_start: 0.7808 (mt0) cc_final: 0.7450 (mm110) REVERT: R 294 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: R 306 MET cc_start: 0.8632 (mmm) cc_final: 0.8247 (mmm) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 1.4081 time to fit residues: 201.5512 Evaluate side-chains 136 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER 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 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 294 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN 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 = 0.4174 r_free = 0.4174 target = 0.175108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119961 restraints weight = 12874.402| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.87 r_work: 0.3387 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10593 Z= 0.236 Angle : 0.556 9.501 14343 Z= 0.287 Chirality : 0.042 0.300 1583 Planarity : 0.004 0.059 1809 Dihedral : 6.682 59.970 1671 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.65 % Allowed : 22.94 % Favored : 75.41 % 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: 0.92 (0.24), residues: 1256 helix: 1.90 (0.23), residues: 524 sheet: 0.25 (0.34), residues: 233 loop : -0.57 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 139 HIS 0.004 0.001 HIS R 302 PHE 0.017 0.002 PHE B 151 TYR 0.013 0.002 TYR A 311 ARG 0.005 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4913.66 seconds wall clock time: 86 minutes 31.57 seconds (5191.57 seconds total)