Starting phenix.real_space_refine on Tue Dec 31 16:55:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnx_45765/12_2024/9cnx_45765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnx_45765/12_2024/9cnx_45765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cnx_45765/12_2024/9cnx_45765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnx_45765/12_2024/9cnx_45765.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnx_45765/12_2024/9cnx_45765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnx_45765/12_2024/9cnx_45765.cif" } resolution = 3.55 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= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5743 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 31 5.16 5 C 7303 2.51 5 N 1986 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11582 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 6025 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 28, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2657 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 11, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 385 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 6, 'TRANS': 47} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1703 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 691 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 119 Unusual residues: {'ACY': 1} Classifications: {'peptide': 13, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="ACY G 0 " pdbres="PHE G 1 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Planarities with less than four sites: {'ACY:plan-1': 1, 'ALN:plan-2': 1, 'MHS:plan-2': 1, 'ABA:plan-1': 1, 'YNM:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.04, per 1000 atoms: 0.61 Number of scatterers: 11582 At special positions: 0 Unit cell: (124.8, 126, 151.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 31 16.00 O 2261 8.00 N 1986 7.00 C 7303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 901 " pdb="ZN ZN G 901 " - pdb=" NE2 MHS G 11 " pdb="ZN ZN G 901 " - pdb=" ND1 HIS G 4 " pdb="ZN ZN G 901 " - pdb=" NE2 HIS G 9 " 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2702 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 25.3% alpha, 29.9% 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 38 through 46 Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.035A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.958A pdb=" N GLY A 118 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.564A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.508A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.740A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.814A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.740A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.869A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.547A pdb=" N VAL A 733 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.668A pdb=" N GLN A 753 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 removed outlier: 3.749A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.657A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 80' Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.954A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.942A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.672A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.829A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.507A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.834A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.407A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.596A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.564A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 7.366A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.744A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 433 removed outlier: 3.759A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 738 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.872A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 removed outlier: 7.234A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.672A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.731A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.917A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.928A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.566A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.512A pdb=" N TRP B 348 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.686A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.686A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1377 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: 3.84 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3857 1.34 - 1.46: 2158 1.46 - 1.57: 5755 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 11831 Sorted by residual: bond pdb=" ND1 MHS G 11 " pdb=" CE1 MHS G 11 " ideal model delta sigma weight residual 1.351 1.399 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" CE1 MHS G 11 " pdb=" NE2 MHS G 11 " ideal model delta sigma weight residual 1.307 1.349 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" CG MHS G 11 " pdb=" CD2 MHS G 11 " ideal model delta sigma weight residual 1.370 1.408 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C ACY G 0 " pdb=" O ACY G 0 " ideal model delta sigma weight residual 1.248 1.286 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" CA VAL D 27 " pdb=" C VAL D 27 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.10e-02 2.27e+03 2.72e+00 ... (remaining 11826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 15807 2.24 - 4.49: 222 4.49 - 6.73: 30 6.73 - 8.97: 10 8.97 - 11.21: 3 Bond angle restraints: 16072 Sorted by residual: angle pdb=" N GLU D 56 " pdb=" CA GLU D 56 " pdb=" CB GLU D 56 " ideal model delta sigma weight residual 110.28 117.40 -7.12 1.55e+00 4.16e-01 2.11e+01 angle pdb=" N ARG G 7 " pdb=" CA ARG G 7 " pdb=" C ARG G 7 " ideal model delta sigma weight residual 111.00 122.21 -11.21 2.80e+00 1.28e-01 1.60e+01 angle pdb=" C ASN D 33 " pdb=" N GLU D 34 " pdb=" CA GLU D 34 " ideal model delta sigma weight residual 122.06 115.15 6.91 1.86e+00 2.89e-01 1.38e+01 angle pdb=" C LEU D 55 " pdb=" N GLU D 56 " pdb=" CA GLU D 56 " ideal model delta sigma weight residual 120.31 114.75 5.56 1.52e+00 4.33e-01 1.34e+01 angle pdb=" CA MET D 109 " pdb=" CB MET D 109 " pdb=" CG MET D 109 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 ... (remaining 16067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6481 17.75 - 35.51: 394 35.51 - 53.26: 69 53.26 - 71.01: 17 71.01 - 88.77: 13 Dihedral angle restraints: 6974 sinusoidal: 2726 harmonic: 4248 Sorted by residual: dihedral pdb=" CA GLN A 495 " pdb=" C GLN A 495 " pdb=" N ALA A 496 " pdb=" CA ALA A 496 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA HIS B 324 " pdb=" C HIS B 324 " pdb=" N ARG B 325 " pdb=" CA ARG B 325 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TRP A 546 " pdb=" C TRP A 546 " pdb=" N ARG A 547 " pdb=" CA ARG A 547 " ideal model delta harmonic sigma weight residual 180.00 163.65 16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1228 0.045 - 0.090: 367 0.090 - 0.135: 140 0.135 - 0.180: 14 0.180 - 0.225: 4 Chirality restraints: 1753 Sorted by residual: chirality pdb=" CB ILE A 94 " pdb=" CA ILE A 94 " pdb=" CG1 ILE A 94 " pdb=" CG2 ILE A 94 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG G 7 " pdb=" N ARG G 7 " pdb=" C ARG G 7 " pdb=" CB ARG G 7 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL E 27 " pdb=" CA VAL E 27 " pdb=" CG1 VAL E 27 " pdb=" CG2 VAL E 27 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1750 not shown) Planarity restraints: 2111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 91 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 92 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 675 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 676 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 248 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 249 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " 0.026 5.00e-02 4.00e+02 ... (remaining 2108 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3563 2.83 - 3.35: 10080 3.35 - 3.86: 17493 3.86 - 4.38: 19747 4.38 - 4.90: 36269 Nonbonded interactions: 87152 Sorted by model distance: nonbonded pdb=" NH1 ARG A 79 " pdb=" O ASP A 80 " model vdw 2.310 3.120 nonbonded pdb=" ND1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 2.331 3.120 nonbonded pdb=" OG1 THR B 309 " pdb=" O GLY B 312 " model vdw 2.342 3.040 nonbonded pdb=" OE1 GLN B 319 " pdb=" NH2 ARG B 355 " model vdw 2.344 3.120 nonbonded pdb=" NE2 GLN D 230 " pdb=" OD1 ASP E 66 " model vdw 2.352 3.120 ... (remaining 87147 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.490 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 0.050 11831 Z= 0.225 Angle : 0.704 11.214 16072 Z= 0.371 Chirality : 0.049 0.225 1753 Planarity : 0.005 0.058 2111 Dihedral : 12.672 88.768 4272 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1454 helix: 0.70 (0.28), residues: 311 sheet: 0.41 (0.24), residues: 445 loop : -0.24 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 93 HIS 0.006 0.001 HIS G 9 PHE 0.026 0.002 PHE A 428 TYR 0.013 0.001 TYR B 123 ARG 0.009 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.9129 (mtp) cc_final: 0.8898 (tpt) REVERT: A 304 MET cc_start: 0.8080 (ttp) cc_final: 0.7861 (ttm) REVERT: A 369 MET cc_start: 0.8647 (mmp) cc_final: 0.8328 (mmp) REVERT: A 459 ASN cc_start: 0.7693 (t0) cc_final: 0.7454 (t0) REVERT: B 48 TRP cc_start: 0.8592 (p-90) cc_final: 0.7676 (p-90) REVERT: D 35 ILE cc_start: 0.9057 (mt) cc_final: 0.8707 (mt) REVERT: D 87 LEU cc_start: 0.9285 (mp) cc_final: 0.9003 (mp) REVERT: E 44 SER cc_start: 0.8788 (p) cc_final: 0.8432 (p) REVERT: E 47 ARG cc_start: 0.7416 (mpt180) cc_final: 0.7080 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2422 time to fit residues: 45.8706 Evaluate side-chains 109 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN G 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11831 Z= 0.198 Angle : 0.562 9.997 16072 Z= 0.300 Chirality : 0.044 0.184 1753 Planarity : 0.004 0.058 2111 Dihedral : 5.059 67.611 1623 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.73 % Allowed : 4.45 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1454 helix: 1.10 (0.29), residues: 311 sheet: 0.62 (0.23), residues: 455 loop : -0.25 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 776 HIS 0.003 0.001 HIS A 30 PHE 0.014 0.001 PHE A 494 TYR 0.013 0.001 TYR D 36 ARG 0.007 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.387 Fit side-chains REVERT: A 109 MET cc_start: 0.9159 (mtp) cc_final: 0.8920 (tpt) REVERT: A 304 MET cc_start: 0.8142 (ttp) cc_final: 0.7922 (ttm) REVERT: A 369 MET cc_start: 0.8593 (mmp) cc_final: 0.8206 (mmp) REVERT: A 614 ASP cc_start: 0.8050 (p0) cc_final: 0.7824 (p0) REVERT: B 48 TRP cc_start: 0.8638 (p-90) cc_final: 0.7657 (p-90) REVERT: B 278 MET cc_start: 0.7669 (mpp) cc_final: 0.7277 (mpp) REVERT: D 35 ILE cc_start: 0.8709 (mt) cc_final: 0.8488 (mt) REVERT: D 42 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8139 (mtmm) REVERT: D 49 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7602 (tpp80) REVERT: D 64 PHE cc_start: 0.8291 (m-10) cc_final: 0.8036 (m-80) REVERT: D 87 LEU cc_start: 0.9305 (mp) cc_final: 0.9063 (mp) REVERT: E 44 SER cc_start: 0.8795 (p) cc_final: 0.8512 (p) REVERT: E 96 ASN cc_start: 0.8309 (t0) cc_final: 0.7796 (p0) outliers start: 9 outliers final: 5 residues processed: 122 average time/residue: 0.2351 time to fit residues: 42.5479 Evaluate side-chains 114 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11831 Z= 0.224 Angle : 0.543 9.465 16072 Z= 0.287 Chirality : 0.043 0.175 1753 Planarity : 0.004 0.063 2111 Dihedral : 4.923 67.717 1623 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.73 % Allowed : 7.20 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1454 helix: 1.50 (0.30), residues: 305 sheet: 0.54 (0.23), residues: 470 loop : -0.21 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 546 HIS 0.005 0.001 HIS E 83 PHE 0.021 0.001 PHE A 426 TYR 0.015 0.001 TYR B 345 ARG 0.007 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.374 Fit side-chains REVERT: A 109 MET cc_start: 0.9265 (mtp) cc_final: 0.8784 (tpt) REVERT: A 304 MET cc_start: 0.8119 (ttp) cc_final: 0.7892 (ttm) REVERT: A 369 MET cc_start: 0.8575 (mmp) cc_final: 0.8248 (mmp) REVERT: B 48 TRP cc_start: 0.8618 (p-90) cc_final: 0.7552 (p-90) REVERT: D 49 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.7571 (tpp80) REVERT: D 64 PHE cc_start: 0.8372 (m-80) cc_final: 0.8072 (m-80) REVERT: D 87 LEU cc_start: 0.9329 (mp) cc_final: 0.9070 (mp) REVERT: E 44 SER cc_start: 0.8772 (p) cc_final: 0.8550 (p) REVERT: E 96 ASN cc_start: 0.8296 (t0) cc_final: 0.7785 (p0) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.2480 time to fit residues: 42.8897 Evaluate side-chains 116 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 0.0030 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11831 Z= 0.136 Angle : 0.494 8.101 16072 Z= 0.260 Chirality : 0.042 0.148 1753 Planarity : 0.004 0.071 2111 Dihedral : 4.614 65.559 1623 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.49 % Allowed : 9.39 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1454 helix: 1.77 (0.29), residues: 310 sheet: 0.65 (0.23), residues: 471 loop : -0.14 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 546 HIS 0.002 0.001 HIS E 83 PHE 0.010 0.001 PHE A 494 TYR 0.011 0.001 TYR B 345 ARG 0.003 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.295 Fit side-chains REVERT: A 109 MET cc_start: 0.9272 (mtp) cc_final: 0.8845 (tpt) REVERT: A 222 ASP cc_start: 0.8168 (m-30) cc_final: 0.7955 (m-30) REVERT: A 304 MET cc_start: 0.8065 (ttp) cc_final: 0.7863 (ttm) REVERT: A 369 MET cc_start: 0.8547 (mmp) cc_final: 0.8225 (mmp) REVERT: B 48 TRP cc_start: 0.8601 (p-90) cc_final: 0.7620 (p-90) REVERT: D 42 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8558 (mtmm) REVERT: D 49 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7520 (tpp80) REVERT: D 64 PHE cc_start: 0.8370 (m-80) cc_final: 0.8058 (m-80) REVERT: D 87 LEU cc_start: 0.9326 (mp) cc_final: 0.9060 (mp) REVERT: D 227 MET cc_start: 0.8364 (mtp) cc_final: 0.7813 (mtp) outliers start: 6 outliers final: 2 residues processed: 118 average time/residue: 0.2393 time to fit residues: 41.7945 Evaluate side-chains 110 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 chunk 0 optimal weight: 50.0000 chunk 72 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11831 Z= 0.269 Angle : 0.548 8.333 16072 Z= 0.289 Chirality : 0.043 0.149 1753 Planarity : 0.004 0.070 2111 Dihedral : 4.761 67.052 1623 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.21 % Allowed : 9.63 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1454 helix: 1.93 (0.30), residues: 310 sheet: 0.47 (0.23), residues: 472 loop : -0.18 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.003 0.001 HIS B 165 PHE 0.035 0.001 PHE A 426 TYR 0.022 0.001 TYR B 333 ARG 0.005 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.370 Fit side-chains REVERT: A 109 MET cc_start: 0.9261 (mtp) cc_final: 0.8832 (tpt) REVERT: A 304 MET cc_start: 0.8114 (ttp) cc_final: 0.7900 (ttm) REVERT: A 545 MET cc_start: 0.8165 (mtp) cc_final: 0.7827 (mtp) REVERT: B 48 TRP cc_start: 0.8600 (p-90) cc_final: 0.7552 (p-90) REVERT: B 278 MET cc_start: 0.8027 (mpp) cc_final: 0.7463 (mpp) REVERT: D 49 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7518 (tpp80) REVERT: D 64 PHE cc_start: 0.8271 (m-80) cc_final: 0.7937 (m-80) REVERT: D 87 LEU cc_start: 0.9334 (mp) cc_final: 0.9057 (mp) REVERT: D 227 MET cc_start: 0.8547 (mtp) cc_final: 0.8214 (mtp) REVERT: E 47 ARG cc_start: 0.7273 (mpt180) cc_final: 0.7056 (mmt-90) REVERT: E 96 ASN cc_start: 0.8269 (t0) cc_final: 0.7800 (p0) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.2378 time to fit residues: 42.6926 Evaluate side-chains 119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11831 Z= 0.194 Angle : 0.526 7.917 16072 Z= 0.277 Chirality : 0.042 0.136 1753 Planarity : 0.004 0.069 2111 Dihedral : 4.638 66.814 1623 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.97 % Allowed : 11.41 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1454 helix: 2.08 (0.30), residues: 307 sheet: 0.50 (0.23), residues: 471 loop : -0.18 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 546 HIS 0.003 0.000 HIS G 9 PHE 0.010 0.001 PHE A 494 TYR 0.013 0.001 TYR B 333 ARG 0.004 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.350 Fit side-chains REVERT: A 109 MET cc_start: 0.9256 (mtp) cc_final: 0.8830 (tpt) REVERT: B 48 TRP cc_start: 0.8615 (p-90) cc_final: 0.7547 (p-90) REVERT: D 42 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8381 (mtmm) REVERT: D 49 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7514 (tpp80) REVERT: D 64 PHE cc_start: 0.8268 (m-80) cc_final: 0.7924 (m-80) REVERT: D 87 LEU cc_start: 0.9326 (mp) cc_final: 0.9041 (mp) REVERT: D 227 MET cc_start: 0.8348 (mtp) cc_final: 0.7990 (mtp) REVERT: E 47 ARG cc_start: 0.7299 (mpt180) cc_final: 0.7049 (mpt180) REVERT: E 96 ASN cc_start: 0.8240 (t0) cc_final: 0.7762 (p0) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 0.2303 time to fit residues: 40.1916 Evaluate side-chains 119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11831 Z= 0.193 Angle : 0.523 8.536 16072 Z= 0.275 Chirality : 0.042 0.135 1753 Planarity : 0.004 0.069 2111 Dihedral : 4.574 66.264 1623 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.38 % Allowed : 11.57 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1454 helix: 2.15 (0.30), residues: 307 sheet: 0.52 (0.23), residues: 471 loop : -0.18 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 546 HIS 0.003 0.000 HIS G 9 PHE 0.009 0.001 PHE A 197 TYR 0.013 0.001 TYR D 36 ARG 0.006 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.266 Fit side-chains REVERT: A 109 MET cc_start: 0.9261 (mtp) cc_final: 0.8838 (tpt) REVERT: A 142 TYR cc_start: 0.7733 (m-10) cc_final: 0.7502 (m-10) REVERT: B 48 TRP cc_start: 0.8639 (p-90) cc_final: 0.7546 (p-90) REVERT: D 42 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8402 (mtmm) REVERT: D 49 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7515 (tpp80) REVERT: D 64 PHE cc_start: 0.8241 (m-80) cc_final: 0.7903 (m-80) REVERT: D 87 LEU cc_start: 0.9329 (mp) cc_final: 0.9041 (mp) REVERT: D 146 ASP cc_start: 0.8063 (t0) cc_final: 0.7853 (t0) REVERT: D 227 MET cc_start: 0.8366 (mtp) cc_final: 0.8013 (mtp) REVERT: E 47 ARG cc_start: 0.7297 (mpt180) cc_final: 0.7036 (mpt180) REVERT: E 54 GLN cc_start: 0.8367 (mt0) cc_final: 0.8155 (mt0) REVERT: E 96 ASN cc_start: 0.8208 (t0) cc_final: 0.7815 (p0) outliers start: 17 outliers final: 13 residues processed: 119 average time/residue: 0.2396 time to fit residues: 42.2152 Evaluate side-chains 121 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11831 Z= 0.255 Angle : 0.555 9.014 16072 Z= 0.291 Chirality : 0.043 0.135 1753 Planarity : 0.004 0.069 2111 Dihedral : 4.646 66.639 1623 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.29 % Allowed : 11.89 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1454 helix: 2.16 (0.30), residues: 307 sheet: 0.44 (0.23), residues: 475 loop : -0.18 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.003 0.001 HIS G 9 PHE 0.010 0.001 PHE A 517 TYR 0.013 0.001 TYR B 345 ARG 0.006 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.9262 (mtp) cc_final: 0.8824 (tpt) REVERT: A 261 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8559 (p) REVERT: B 48 TRP cc_start: 0.8648 (p-90) cc_final: 0.7597 (p-90) REVERT: D 42 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8444 (mtmm) REVERT: D 49 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7519 (tpp80) REVERT: D 64 PHE cc_start: 0.8268 (m-80) cc_final: 0.8058 (m-10) REVERT: D 87 LEU cc_start: 0.9333 (mp) cc_final: 0.9044 (mp) REVERT: E 47 ARG cc_start: 0.7308 (mpt180) cc_final: 0.7057 (mpt180) REVERT: E 54 GLN cc_start: 0.8378 (mt0) cc_final: 0.8146 (mt0) REVERT: E 96 ASN cc_start: 0.8226 (t0) cc_final: 0.7805 (p0) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.2262 time to fit residues: 39.7708 Evaluate side-chains 120 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11831 Z= 0.202 Angle : 0.533 9.322 16072 Z= 0.278 Chirality : 0.042 0.137 1753 Planarity : 0.004 0.068 2111 Dihedral : 4.547 66.304 1623 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1454 helix: 2.13 (0.30), residues: 312 sheet: 0.60 (0.24), residues: 451 loop : -0.11 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 546 HIS 0.002 0.000 HIS G 9 PHE 0.011 0.001 PHE A 648 TYR 0.015 0.001 TYR D 36 ARG 0.007 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.273 Fit side-chains REVERT: A 109 MET cc_start: 0.9256 (mtp) cc_final: 0.8766 (tpt) REVERT: B 48 TRP cc_start: 0.8653 (p-90) cc_final: 0.7607 (p-90) REVERT: D 49 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7507 (tpp80) REVERT: D 64 PHE cc_start: 0.8257 (m-80) cc_final: 0.8046 (m-10) REVERT: D 87 LEU cc_start: 0.9330 (mp) cc_final: 0.9038 (mp) REVERT: E 47 ARG cc_start: 0.7305 (mpt180) cc_final: 0.7036 (mpt180) REVERT: E 54 GLN cc_start: 0.8367 (mt0) cc_final: 0.8148 (mt0) REVERT: E 96 ASN cc_start: 0.8205 (t0) cc_final: 0.7816 (p0) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.2343 time to fit residues: 40.5313 Evaluate side-chains 120 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 0.0970 chunk 115 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11831 Z= 0.198 Angle : 0.551 10.359 16072 Z= 0.286 Chirality : 0.043 0.143 1753 Planarity : 0.004 0.067 2111 Dihedral : 4.523 65.722 1623 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.13 % Allowed : 12.38 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1454 helix: 2.06 (0.29), residues: 315 sheet: 0.60 (0.24), residues: 452 loop : -0.09 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.003 0.001 HIS E 83 PHE 0.010 0.001 PHE A 648 TYR 0.013 0.001 TYR B 345 ARG 0.007 0.000 ARG C 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.262 Fit side-chains REVERT: A 109 MET cc_start: 0.9237 (mtp) cc_final: 0.8749 (tpt) REVERT: A 261 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8542 (p) REVERT: B 48 TRP cc_start: 0.8652 (p-90) cc_final: 0.7603 (p-90) REVERT: D 49 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7500 (tpp80) REVERT: D 64 PHE cc_start: 0.8244 (m-80) cc_final: 0.8036 (m-10) REVERT: D 87 LEU cc_start: 0.9329 (mp) cc_final: 0.9039 (mp) REVERT: E 47 ARG cc_start: 0.7332 (mpt180) cc_final: 0.7077 (mpt180) REVERT: E 54 GLN cc_start: 0.8370 (mt0) cc_final: 0.8129 (mt0) REVERT: E 96 ASN cc_start: 0.8196 (t0) cc_final: 0.7816 (p0) outliers start: 14 outliers final: 12 residues processed: 117 average time/residue: 0.2334 time to fit residues: 40.9252 Evaluate side-chains 121 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075519 restraints weight = 24544.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.074868 restraints weight = 15933.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075590 restraints weight = 14390.802| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11831 Z= 0.301 Angle : 0.584 13.594 16072 Z= 0.304 Chirality : 0.044 0.140 1753 Planarity : 0.004 0.066 2111 Dihedral : 4.675 66.641 1623 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 12.22 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1454 helix: 2.06 (0.30), residues: 313 sheet: 0.47 (0.23), residues: 455 loop : -0.13 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.004 0.001 HIS G 9 PHE 0.015 0.001 PHE A 517 TYR 0.016 0.002 TYR D 36 ARG 0.007 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.43 seconds wall clock time: 40 minutes 10.64 seconds (2410.64 seconds total)