Starting phenix.real_space_refine on Wed Feb 12 08:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djp_7939/02_2025/6djp_7939.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djp_7939/02_2025/6djp_7939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6djp_7939/02_2025/6djp_7939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djp_7939/02_2025/6djp_7939.map" model { file = "/net/cci-nas-00/data/ceres_data/6djp_7939/02_2025/6djp_7939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djp_7939/02_2025/6djp_7939.cif" } resolution = 4.8 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= 0.016 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: 3 Type Number sf(0) Gaussians C 4368 2.51 5 N 1421 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7307 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 2979 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 28, 'TRANS': 564} Unresolved non-hydrogen bonds: 1693 Unresolved non-hydrogen angles: 2167 Unresolved non-hydrogen dihedrals: 1414 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 4, 'TYR:plan': 26, 'ASN:plan1': 18, 'TRP:plan': 5, 'ASP:plan': 47, 'PHE:plan': 37, 'GLU:plan': 22, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 1027 Chain: "B" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1791 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1013 Unresolved non-hydrogen angles: 1297 Unresolved non-hydrogen dihedrals: 829 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 15, 'TYR:plan': 12, 'ASN:plan1': 22, 'TRP:plan': 2, 'HIS:plan': 13, 'PHE:plan': 12, 'GLU:plan': 22, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 536 Chain: "C" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 239 Chain: "D" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 536 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 152 Chain: "E" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 569 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 209 Chain: "F" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 172 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.05, per 1000 atoms: 0.69 Number of scatterers: 7307 At special positions: 0 Unit cell: (96.86, 126.92, 172.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1518 8.00 N 1421 7.00 C 4368 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=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 6 " ALPHA1-4 " MAN I 4 " - " MAN I 5 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A1011 " - " ASN A 524 " " NAG B 701 " - " ASN B 379 " " NAG G 1 " - " ASN A 44 " " NAG H 1 " - " ASN A 260 " " NAG I 1 " - " ASN A 266 " " NAG J 1 " - " ASN A 585 " " NAG K 1 " - " ASN B 191 " " NAG L 1 " - " ASN B 360 " " NAG M 1 " - " ASN B 389 " " NAG N 1 " - " ASN B 414 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 10.8% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 339 through 342 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 136 removed outlier: 4.805A pdb=" N LYS B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N SER B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 303 through 313 removed outlier: 3.980A pdb=" N HIS B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TRP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 344 removed outlier: 4.322A pdb=" N VAL B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.309A pdb=" N ALA D 82 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.019A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 411 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 7.008A pdb=" N ASP A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 101 removed outlier: 3.608A pdb=" N SER A 97 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.749A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 229 removed outlier: 3.658A pdb=" N SER A 225 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 283 removed outlier: 3.751A pdb=" N SER A 279 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 348 removed outlier: 5.935A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB3, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AB6, first strand: chain 'B' and resid 81 through 84 removed outlier: 5.559A pdb=" N ILE B 419 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA B 406 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE B 421 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 404 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 97 Processing sheet with id=AB8, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.260A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AC2, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.379A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC6, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.840A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.084A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.484A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.484A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1422 1.29 - 1.36: 1416 1.36 - 1.43: 65 1.43 - 1.51: 1855 1.51 - 1.58: 2604 Bond restraints: 7362 Sorted by residual: bond pdb=" C GLY B 376 " pdb=" N CYS B 377 " ideal model delta sigma weight residual 1.330 1.241 0.089 1.45e-02 4.76e+03 3.75e+01 bond pdb=" N PRO B 78 " pdb=" CD PRO B 78 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.52e+01 bond pdb=" C GLU B 385 " pdb=" N VAL B 386 " ideal model delta sigma weight residual 1.329 1.393 -0.064 1.69e-02 3.50e+03 1.46e+01 bond pdb=" CA ILE A 555 " pdb=" C ILE A 555 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.16e-02 7.43e+03 1.41e+01 bond pdb=" CA LEU F 11 " pdb=" C LEU F 11 " ideal model delta sigma weight residual 1.523 1.481 0.043 1.18e-02 7.18e+03 1.30e+01 ... (remaining 7357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 9366 3.45 - 6.90: 814 6.90 - 10.34: 73 10.34 - 13.79: 5 13.79 - 17.24: 1 Bond angle restraints: 10259 Sorted by residual: angle pdb=" N ARG F 61 " pdb=" CA ARG F 61 " pdb=" C ARG F 61 " ideal model delta sigma weight residual 114.56 102.74 11.82 1.27e+00 6.20e-01 8.66e+01 angle pdb=" C MET A 400 " pdb=" N PRO A 401 " pdb=" CA PRO A 401 " ideal model delta sigma weight residual 119.66 126.19 -6.53 7.30e-01 1.88e+00 8.01e+01 angle pdb=" N TYR F 32 " pdb=" CA TYR F 32 " pdb=" C TYR F 32 " ideal model delta sigma weight residual 108.60 121.42 -12.82 1.46e+00 4.69e-01 7.71e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 128.35 -8.79 1.02e+00 9.61e-01 7.43e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.33 -8.77 1.02e+00 9.61e-01 7.40e+01 ... (remaining 10254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 4540 21.64 - 43.27: 48 43.27 - 64.91: 7 64.91 - 86.54: 10 86.54 - 108.18: 8 Dihedral angle restraints: 4613 sinusoidal: 679 harmonic: 3934 Sorted by residual: dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.47 108.18 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.69 107.31 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.44 107.15 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1203 0.108 - 0.216: 162 0.216 - 0.324: 20 0.324 - 0.432: 2 0.432 - 0.540: 2 Chirality restraints: 1389 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.92e+01 chirality pdb=" C1 MAN I 5 " pdb=" O4 MAN I 4 " pdb=" C2 MAN I 5 " pdb=" O5 MAN I 5 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-02 2.50e+03 4.09e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.69e+01 ... (remaining 1386 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.051 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" C7 NAG M 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.068 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " 0.034 2.00e-02 2.50e+03 3.45e-02 1.49e+01 pdb=" CG ASN A 524 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.053 2.00e-02 2.50e+03 pdb=" C1 NAG A1011 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.040 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" C7 NAG N 2 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.051 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2968 2.87 - 3.38: 6035 3.38 - 3.89: 9738 3.89 - 4.39: 9675 4.39 - 4.90: 16905 Nonbonded interactions: 45321 Sorted by model distance: nonbonded pdb=" N ARG F 61 " pdb=" N PHE F 62 " model vdw 2.368 2.560 nonbonded pdb=" N SER C 59 " pdb=" O SER C 59 " model vdw 2.447 2.496 nonbonded pdb=" O4 NAG G 2 " pdb=" O6 NAG G 2 " model vdw 2.450 3.040 nonbonded pdb=" N GLU A 367 " pdb=" O GLU A 367 " model vdw 2.457 2.496 nonbonded pdb=" O4 NAG M 2 " pdb=" O6 NAG M 2 " model vdw 2.457 3.040 ... (remaining 45316 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 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.740 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 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 : 0.012 0.089 7362 Z= 0.891 Angle : 2.010 17.240 10259 Z= 1.345 Chirality : 0.079 0.540 1389 Planarity : 0.009 0.042 1476 Dihedral : 11.307 108.175 2065 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1379 helix: -1.92 (0.42), residues: 107 sheet: -0.01 (0.22), residues: 477 loop : -0.52 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.743 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0727 time to fit residues: 5.3253 Evaluate side-chains 30 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.0010 chunk 55 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.107599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.091767 restraints weight = 43182.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092453 restraints weight = 37402.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093215 restraints weight = 32175.341| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7362 Z= 0.217 Angle : 0.716 13.713 10259 Z= 0.368 Chirality : 0.050 0.284 1389 Planarity : 0.004 0.050 1476 Dihedral : 8.758 79.531 1859 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: -0.21 (0.22), residues: 1379 helix: -0.17 (0.54), residues: 97 sheet: 0.15 (0.22), residues: 503 loop : -0.24 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.797 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0658 time to fit residues: 5.0622 Evaluate side-chains 31 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 6 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 2 optimal weight: 8.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.095990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.079382 restraints weight = 43136.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079633 restraints weight = 35797.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080257 restraints weight = 32853.467| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 7362 Z= 0.300 Angle : 0.760 12.197 10259 Z= 0.403 Chirality : 0.049 0.219 1389 Planarity : 0.005 0.048 1476 Dihedral : 8.500 67.687 1859 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 1379 helix: -0.50 (0.51), residues: 105 sheet: 0.09 (0.23), residues: 503 loop : -0.91 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.759 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0655 time to fit residues: 4.6240 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 116 optimal weight: 0.0870 chunk 131 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 1.6562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.076910 restraints weight = 42842.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077802 restraints weight = 34549.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078494 restraints weight = 29042.697| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7362 Z= 0.228 Angle : 0.667 11.020 10259 Z= 0.344 Chirality : 0.048 0.277 1389 Planarity : 0.005 0.044 1476 Dihedral : 7.738 56.920 1859 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 (0.23), residues: 1379 helix: 0.05 (0.56), residues: 99 sheet: -0.14 (0.22), residues: 508 loop : -1.00 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.846 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0660 time to fit residues: 4.6592 Evaluate side-chains 29 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.2980 chunk 35 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.091678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074520 restraints weight = 42825.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075411 restraints weight = 34747.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076104 restraints weight = 29370.247| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 7362 Z= 0.253 Angle : 0.692 10.508 10259 Z= 0.355 Chirality : 0.048 0.240 1389 Planarity : 0.005 0.044 1476 Dihedral : 7.818 54.576 1859 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1379 helix: 0.22 (0.56), residues: 98 sheet: -0.31 (0.23), residues: 495 loop : -1.13 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.708 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0685 time to fit residues: 4.7748 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065736 restraints weight = 45257.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065969 restraints weight = 37475.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.066318 restraints weight = 34283.433| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.9015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.259 7362 Z= 0.803 Angle : 1.401 18.248 10259 Z= 0.771 Chirality : 0.060 0.349 1389 Planarity : 0.009 0.066 1476 Dihedral : 12.236 59.984 1859 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.19 % Favored : 82.31 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.98 % 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: -3.58 (0.20), residues: 1379 helix: -3.19 (0.37), residues: 84 sheet: -1.51 (0.24), residues: 425 loop : -2.91 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.807 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0680 time to fit residues: 4.7078 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068476 restraints weight = 43963.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069316 restraints weight = 35015.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070015 restraints weight = 29296.260| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.8818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 7362 Z= 0.335 Angle : 0.849 14.025 10259 Z= 0.448 Chirality : 0.050 0.312 1389 Planarity : 0.006 0.049 1476 Dihedral : 10.023 58.095 1859 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.29 (0.21), residues: 1379 helix: -2.00 (0.44), residues: 94 sheet: -1.53 (0.24), residues: 430 loop : -2.68 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.830 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0717 time to fit residues: 4.8511 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 45 optimal weight: 0.0060 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 2.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068502 restraints weight = 44558.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068563 restraints weight = 37016.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069212 restraints weight = 33949.230| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.9349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 7362 Z= 0.376 Angle : 0.868 13.886 10259 Z= 0.462 Chirality : 0.050 0.327 1389 Planarity : 0.006 0.052 1476 Dihedral : 10.006 58.525 1859 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % Favored : 83.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.32 (0.21), residues: 1379 helix: -1.85 (0.47), residues: 91 sheet: -1.49 (0.26), residues: 394 loop : -2.74 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.830 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0673 time to fit residues: 4.6883 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 51 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068058 restraints weight = 44515.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068944 restraints weight = 35598.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069675 restraints weight = 29483.282| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.9529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7362 Z= 0.305 Angle : 0.795 17.742 10259 Z= 0.414 Chirality : 0.048 0.309 1389 Planarity : 0.006 0.046 1476 Dihedral : 9.314 58.658 1859 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.26 (0.22), residues: 1379 helix: -1.46 (0.49), residues: 91 sheet: -1.53 (0.26), residues: 401 loop : -2.70 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.765 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0673 time to fit residues: 4.6451 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.066136 restraints weight = 45785.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066786 restraints weight = 37581.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067281 restraints weight = 30787.348| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 1.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.162 7362 Z= 0.493 Angle : 1.003 16.035 10259 Z= 0.536 Chirality : 0.052 0.365 1389 Planarity : 0.007 0.053 1476 Dihedral : 10.647 59.825 1859 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 21.03 % Favored : 78.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.87 (0.21), residues: 1379 helix: -2.41 (0.44), residues: 91 sheet: -1.93 (0.25), residues: 396 loop : -3.06 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.786 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0733 time to fit residues: 4.9402 Evaluate side-chains 28 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 53 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069106 restraints weight = 44296.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069275 restraints weight = 35567.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.069728 restraints weight = 32666.586| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 7362 Z= 0.294 Angle : 0.793 15.876 10259 Z= 0.412 Chirality : 0.048 0.318 1389 Planarity : 0.006 0.045 1476 Dihedral : 9.524 59.344 1859 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.57 (0.21), residues: 1379 helix: -1.60 (0.49), residues: 91 sheet: -1.86 (0.25), residues: 407 loop : -2.86 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 61 PHE 0.000 0.000 PHE A 1 TYR 0.000 0.000 TYR A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.93 seconds wall clock time: 33 minutes 49.44 seconds (2029.44 seconds total)