Starting phenix.real_space_refine on Fri Sep 11 04:22:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_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 { model { file = "/net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6djp_7939/09_2026/6djp_7939.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'PHE:plan': 37, 'ASN:plan1': 18, 'ASP:plan': 47, 'GLU:plan': 22, 'TYR:plan': 26, 'ARG:plan': 31, 'GLN:plan1': 30, 'TRP:plan': 5, 'HIS:plan': 4} 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: {'GLU:plan': 22, 'TYR:plan': 12, 'HIS:plan': 13, 'ASN:plan1': 22, 'GLN:plan1': 12, 'ARG:plan': 10, 'PHE:plan': 12, 'ASP:plan': 15, 'TRP:plan': 2} 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: {'GLU:plan': 6, 'GLN:plan1': 5, 'TYR:plan': 10, 'TRP:plan': 4, 'ASN:plan1': 7, 'ARG:plan': 4, 'PHE:plan': 5, 'ASP:plan': 6} 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: {'GLU:plan': 5, 'GLN:plan1': 4, 'PHE:plan': 3, 'TYR:plan': 6, 'HIS:plan': 2, 'TRP:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} 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: {'GLU:plan': 6, 'GLN:plan1': 6, 'TYR:plan': 7, 'PHE:plan': 2, 'TRP:plan': 6, 'ARG:plan': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'ASN:plan1': 3} 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: {'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 9, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2} 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 1.88, per 1000 atoms: 0.26 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: 0.82 Conformation dependent library (CDL) restraints added in 509.4 milliseconds 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: 0.24 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: 1.44 Time building geometry restraints manager: 1.02 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 - 9.89: 4098 9.89 - 19.79: 33 19.79 - 29.68: 6 29.68 - 39.57: 1 39.57 - 49.46: 2 Dihedral angle restraints: 4140 sinusoidal: 206 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASN C 61 " pdb=" C ASN C 61 " pdb=" N PRO C 62 " pdb=" CA PRO C 62 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLY A 173 " pdb=" C GLY A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N ASN A 524 " pdb=" CA ASN A 524 " pdb=" CB ASN A 524 " pdb=" CG ASN A 524 " ideal model delta sinusoidal sigma weight residual -60.00 -109.46 49.46 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 4137 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: 1.080 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 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 7385 Z= 0.815 Angle : 2.022 17.240 10328 Z= 1.344 Chirality : 0.079 0.540 1389 Planarity : 0.009 0.042 1476 Dihedral : 4.717 49.465 1592 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.81 ( 7362) covalent geometry : angle 2.00986 / 1.35 (10259) hydrogen bonds : bond 0.16264 / 11.89 ( 369) hydrogen bonds : angle 9.33679 / 6.77 ( 939) link_ALPHA1-3 : bond 0.04582 / 2.41 ( 1) link_ALPHA1-3 : angle 3.12491 / 1.65 ( 3) link_ALPHA1-4 : bond 0.04724 / 2.49 ( 1) link_ALPHA1-4 : angle 3.55752 / 1.87 ( 3) link_ALPHA1-6 : bond 0.02959 / 1.56 ( 1) link_ALPHA1-6 : angle 2.31754 / 1.23 ( 3) link_BETA1-4 : bond 0.03712 / 2.39 ( 10) link_BETA1-4 : angle 4.44525 / 2.97 ( 30) link_NAG-ASN : bond 0.03097 / 1.93 ( 10) link_NAG-ASN : angle 1.95909 / 1.45 ( 30) *********************** 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 : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0304 time to fit residues: 2.2472 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.092460 restraints weight = 43960.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093326 restraints weight = 37218.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093996 restraints weight = 32039.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094500 restraints weight = 27943.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095119 restraints weight = 23316.584| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7385 Z= 0.153 Angle : 0.739 13.259 10328 Z= 0.372 Chirality : 0.049 0.291 1389 Planarity : 0.004 0.051 1476 Dihedral : 5.078 24.866 1386 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1379 helix: -0.06 (0.54), residues: 97 sheet: 0.15 (0.22), residues: 503 loop : -0.25 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 7362) covalent geometry : angle 0.69486 / 0.36 (10259) hydrogen bonds : bond 0.03736 / 2.77 ( 369) hydrogen bonds : angle 6.74385 / 4.89 ( 939) link_ALPHA1-3 : bond 0.00833 / 0.44 ( 1) link_ALPHA1-3 : angle 1.42922 / 0.67 ( 3) link_ALPHA1-4 : bond 0.00692 / 0.36 ( 1) link_ALPHA1-4 : angle 1.72439 / 1.00 ( 3) link_ALPHA1-6 : bond 0.00046 / 0.02 ( 1) link_ALPHA1-6 : angle 2.36706 / 1.39 ( 3) link_BETA1-4 : bond 0.00821 / 0.48 ( 10) link_BETA1-4 : angle 3.67683 / 2.39 ( 30) link_NAG-ASN : bond 0.00470 / 0.26 ( 10) link_NAG-ASN : angle 2.91328 / 2.03 ( 30) *********************** 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 : 0.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0294 time to fit residues: 2.0696 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.078574 restraints weight = 42919.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079372 restraints weight = 35505.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079654 restraints weight = 30070.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080295 restraints weight = 26458.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080558 restraints weight = 22482.044| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 7385 Z= 0.288 Angle : 0.885 12.141 10328 Z= 0.459 Chirality : 0.049 0.197 1389 Planarity : 0.005 0.048 1476 Dihedral : 6.539 23.852 1386 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.22), residues: 1379 helix: -0.59 (0.51), residues: 98 sheet: -0.07 (0.23), residues: 511 loop : -1.01 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.29 ( 7362) covalent geometry : angle 0.84473 / 0.45 (10259) hydrogen bonds : bond 0.05247 / 3.94 ( 369) hydrogen bonds : angle 7.69302 / 5.62 ( 939) link_ALPHA1-3 : bond 0.00060 / 0.03 ( 1) link_ALPHA1-3 : angle 2.87694 / 1.45 ( 3) link_ALPHA1-4 : bond 0.00679 / 0.36 ( 1) link_ALPHA1-4 : angle 1.72013 / 0.85 ( 3) link_ALPHA1-6 : bond 0.00098 / 0.05 ( 1) link_ALPHA1-6 : angle 2.54868 / 1.36 ( 3) link_BETA1-4 : bond 0.00966 / 0.56 ( 10) link_BETA1-4 : angle 3.64509 / 2.32 ( 30) link_NAG-ASN : bond 0.00821 / 0.51 ( 10) link_NAG-ASN : angle 3.23446 / 2.13 ( 30) *********************** 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 29 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0321 time to fit residues: 2.1352 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 73 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.093849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076578 restraints weight = 43377.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.077481 restraints weight = 34804.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078241 restraints weight = 29253.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078763 restraints weight = 25324.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079241 restraints weight = 22698.580| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7385 Z= 0.186 Angle : 0.705 11.834 10328 Z= 0.352 Chirality : 0.046 0.208 1389 Planarity : 0.005 0.042 1476 Dihedral : 5.460 24.282 1386 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1379 helix: -0.28 (0.53), residues: 105 sheet: -0.12 (0.23), residues: 492 loop : -1.10 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.19 ( 7362) covalent geometry : angle 0.67687 / 0.35 (10259) hydrogen bonds : bond 0.03589 / 2.67 ( 369) hydrogen bonds : angle 6.83021 / 5.00 ( 939) link_ALPHA1-3 : bond 0.00839 / 0.44 ( 1) link_ALPHA1-3 : angle 0.96343 / 0.51 ( 3) link_ALPHA1-4 : bond 0.00194 / 0.10 ( 1) link_ALPHA1-4 : angle 1.45803 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00292 / 0.15 ( 1) link_ALPHA1-6 : angle 1.93545 / 1.14 ( 3) link_BETA1-4 : bond 0.00628 / 0.42 ( 10) link_BETA1-4 : angle 2.71418 / 1.78 ( 30) link_NAG-ASN : bond 0.00687 / 0.40 ( 10) link_NAG-ASN : angle 2.49662 / 1.73 ( 30) *********************** 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 : 0.266 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0264 time to fit residues: 1.7580 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 : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070549 restraints weight = 44154.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071256 restraints weight = 36105.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.071490 restraints weight = 30892.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071874 restraints weight = 27596.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.072247 restraints weight = 24701.193| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 7385 Z= 0.349 Angle : 1.076 24.088 10328 Z= 0.542 Chirality : 0.051 0.286 1389 Planarity : 0.006 0.053 1476 Dihedral : 7.936 29.881 1386 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.47 % Favored : 87.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.22), residues: 1379 helix: -0.98 (0.52), residues: 87 sheet: -0.93 (0.23), residues: 492 loop : -1.90 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.35 ( 7362) covalent geometry : angle 0.99907 / 0.53 (10259) hydrogen bonds : bond 0.05981 / 4.47 ( 369) hydrogen bonds : angle 9.04880 / 6.59 ( 939) link_ALPHA1-3 : bond 0.00432 / 0.23 ( 1) link_ALPHA1-3 : angle 2.28088 / 1.20 ( 3) link_ALPHA1-4 : bond 0.00925 / 0.49 ( 1) link_ALPHA1-4 : angle 2.26905 / 1.06 ( 3) link_ALPHA1-6 : bond 0.00523 / 0.28 ( 1) link_ALPHA1-6 : angle 3.39375 / 1.88 ( 3) link_BETA1-4 : bond 0.01125 / 0.67 ( 10) link_BETA1-4 : angle 4.04857 / 2.52 ( 30) link_NAG-ASN : bond 0.01265 / 0.77 ( 10) link_NAG-ASN : angle 6.24457 / 4.09 ( 30) *********************** 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 27 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0314 time to fit residues: 1.9846 Evaluate side-chains 27 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 106 optimal weight: 0.0060 chunk 104 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.073183 restraints weight = 43656.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074053 restraints weight = 34971.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.074417 restraints weight = 29717.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074872 restraints weight = 25132.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075277 restraints weight = 22661.551| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7385 Z= 0.177 Angle : 0.751 11.640 10328 Z= 0.369 Chirality : 0.048 0.403 1389 Planarity : 0.005 0.045 1476 Dihedral : 6.212 27.468 1386 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.23), residues: 1379 helix: -0.36 (0.54), residues: 99 sheet: -0.96 (0.23), residues: 491 loop : -1.59 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.18 ( 7362) covalent geometry : angle 0.70719 / 0.36 (10259) hydrogen bonds : bond 0.03801 / 2.83 ( 369) hydrogen bonds : angle 7.53763 / 5.49 ( 939) link_ALPHA1-3 : bond 0.00248 / 0.13 ( 1) link_ALPHA1-3 : angle 1.12444 / 0.59 ( 3) link_ALPHA1-4 : bond 0.00155 / 0.08 ( 1) link_ALPHA1-4 : angle 1.46728 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00088 / 0.05 ( 1) link_ALPHA1-6 : angle 1.78553 / 1.02 ( 3) link_BETA1-4 : bond 0.00705 / 0.47 ( 10) link_BETA1-4 : angle 2.74344 / 1.80 ( 30) link_NAG-ASN : bond 0.00815 / 0.49 ( 10) link_NAG-ASN : angle 3.84665 / 2.64 ( 30) *********************** 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 : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0323 time to fit residues: 2.0175 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 52 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 120 optimal weight: 0.0670 chunk 46 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.082073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.066960 restraints weight = 45256.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067419 restraints weight = 35812.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067736 restraints weight = 32408.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068345 restraints weight = 27294.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068760 restraints weight = 22974.183| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.9194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.182 7385 Z= 0.470 Angle : 1.227 16.515 10328 Z= 0.640 Chirality : 0.055 0.380 1389 Planarity : 0.007 0.060 1476 Dihedral : 9.386 43.671 1386 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 18.27 % Favored : 81.29 % 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 : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.21), residues: 1379 helix: -2.33 (0.43), residues: 85 sheet: -1.55 (0.25), residues: 414 loop : -2.72 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00783 / 0.47 ( 7362) covalent geometry : angle 1.16935 / 0.63 (10259) hydrogen bonds : bond 0.07458 / 5.59 ( 369) hydrogen bonds : angle 10.45660 / 7.58 ( 939) link_ALPHA1-3 : bond 0.00738 / 0.39 ( 1) link_ALPHA1-3 : angle 1.52832 / 0.88 ( 3) link_ALPHA1-4 : bond 0.00833 / 0.44 ( 1) link_ALPHA1-4 : angle 2.32467 / 1.09 ( 3) link_ALPHA1-6 : bond 0.00626 / 0.33 ( 1) link_ALPHA1-6 : angle 3.34314 / 1.92 ( 3) link_BETA1-4 : bond 0.01418 / 0.89 ( 10) link_BETA1-4 : angle 4.54517 / 2.83 ( 30) link_NAG-ASN : bond 0.01902 / 1.15 ( 10) link_NAG-ASN : angle 5.34133 / 3.62 ( 30) *********************** 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 : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0318 time to fit residues: 2.0783 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.069978 restraints weight = 44255.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070782 restraints weight = 35525.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071378 restraints weight = 29713.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072019 restraints weight = 25701.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072384 restraints weight = 22952.389| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.8930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 7385 Z= 0.195 Angle : 0.804 14.904 10328 Z= 0.398 Chirality : 0.048 0.298 1389 Planarity : 0.005 0.046 1476 Dihedral : 6.929 29.527 1386 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.22), residues: 1379 helix: -1.11 (0.51), residues: 98 sheet: -1.58 (0.24), residues: 460 loop : -2.42 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.19 ( 7362) covalent geometry : angle 0.76507 / 0.39 (10259) hydrogen bonds : bond 0.04091 / 3.07 ( 369) hydrogen bonds : angle 8.41218 / 6.14 ( 939) link_ALPHA1-3 : bond 0.00031 / 0.02 ( 1) link_ALPHA1-3 : angle 1.14525 / 0.62 ( 3) link_ALPHA1-4 : bond 0.00004 / 0.00 ( 1) link_ALPHA1-4 : angle 1.40362 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00088 / 0.05 ( 1) link_ALPHA1-6 : angle 1.67735 / 0.96 ( 3) link_BETA1-4 : bond 0.00692 / 0.47 ( 10) link_BETA1-4 : angle 2.85571 / 1.89 ( 30) link_NAG-ASN : bond 0.00813 / 0.49 ( 10) link_NAG-ASN : angle 3.68510 / 2.50 ( 30) *********************** 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 : 0.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0309 time to fit residues: 2.0022 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067846 restraints weight = 44224.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068079 restraints weight = 36800.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068707 restraints weight = 33363.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069343 restraints weight = 27354.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069554 restraints weight = 22432.237| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.9467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 7385 Z= 0.315 Angle : 0.955 14.239 10328 Z= 0.487 Chirality : 0.050 0.320 1389 Planarity : 0.006 0.051 1476 Dihedral : 7.808 32.710 1386 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.90 % Favored : 83.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.21), residues: 1379 helix: -1.71 (0.47), residues: 92 sheet: -1.52 (0.25), residues: 406 loop : -2.69 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.31 ( 7362) covalent geometry : angle 0.91119 / 0.48 (10259) hydrogen bonds : bond 0.05472 / 4.11 ( 369) hydrogen bonds : angle 9.20934 / 6.70 ( 939) link_ALPHA1-3 : bond 0.00471 / 0.25 ( 1) link_ALPHA1-3 : angle 1.62061 / 0.92 ( 3) link_ALPHA1-4 : bond 0.00826 / 0.43 ( 1) link_ALPHA1-4 : angle 1.84223 / 0.83 ( 3) link_ALPHA1-6 : bond 0.00353 / 0.19 ( 1) link_ALPHA1-6 : angle 2.50889 / 1.43 ( 3) link_BETA1-4 : bond 0.00891 / 0.59 ( 10) link_BETA1-4 : angle 3.43354 / 2.19 ( 30) link_NAG-ASN : bond 0.01177 / 0.72 ( 10) link_NAG-ASN : angle 4.16267 / 2.80 ( 30) *********************** 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 : 0.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0278 time to fit residues: 1.8222 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 : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 121 optimal weight: 0.0370 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067122 restraints weight = 44896.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067779 restraints weight = 36682.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068192 restraints weight = 30612.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068853 restraints weight = 25981.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.069048 restraints weight = 21581.265| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 1.0110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 7385 Z= 0.331 Angle : 0.995 19.901 10328 Z= 0.505 Chirality : 0.051 0.338 1389 Planarity : 0.006 0.050 1476 Dihedral : 8.142 34.878 1386 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.55 % Favored : 82.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.21), residues: 1379 helix: -1.85 (0.49), residues: 85 sheet: -1.90 (0.25), residues: 406 loop : -3.03 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.33 ( 7362) covalent geometry : angle 0.95190 / 0.50 (10259) hydrogen bonds : bond 0.05727 / 4.32 ( 369) hydrogen bonds : angle 9.64168 / 7.04 ( 939) link_ALPHA1-3 : bond 0.00405 / 0.21 ( 1) link_ALPHA1-3 : angle 1.89788 / 1.08 ( 3) link_ALPHA1-4 : bond 0.00402 / 0.21 ( 1) link_ALPHA1-4 : angle 1.63238 / 0.75 ( 3) link_ALPHA1-6 : bond 0.00095 / 0.05 ( 1) link_ALPHA1-6 : angle 2.17829 / 1.27 ( 3) link_BETA1-4 : bond 0.00786 / 0.53 ( 10) link_BETA1-4 : angle 3.26080 / 2.11 ( 30) link_NAG-ASN : bond 0.01225 / 0.76 ( 10) link_NAG-ASN : angle 4.40693 / 2.94 ( 30) ********************** 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 : 0.289 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0324 time to fit residues: 2.0959 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 : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 105 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 131 optimal weight: 0.0050 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067201 restraints weight = 44655.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.067729 restraints weight = 36097.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068260 restraints weight = 30052.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068821 restraints weight = 26044.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.069109 restraints weight = 21367.821| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 1.0403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 7385 Z= 0.320 Angle : 0.970 15.603 10328 Z= 0.493 Chirality : 0.050 0.317 1389 Planarity : 0.006 0.056 1476 Dihedral : 7.945 34.338 1386 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 19.43 % Favored : 80.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.21), residues: 1379 helix: -1.85 (0.48), residues: 85 sheet: -2.00 (0.25), residues: 404 loop : -3.13 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 11 PHE 0.000 0.000 PHE A 1 TRP 0.000 0.000 TRP A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.32 ( 7362) covalent geometry : angle 0.92613 / 0.48 (10259) hydrogen bonds : bond 0.05559 / 4.19 ( 369) hydrogen bonds : angle 9.49516 / 6.93 ( 939) link_ALPHA1-3 : bond 0.00424 / 0.22 ( 1) link_ALPHA1-3 : angle 1.60394 / 0.91 ( 3) link_ALPHA1-4 : bond 0.00514 / 0.27 ( 1) link_ALPHA1-4 : angle 1.82764 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00071 / 0.04 ( 1) link_ALPHA1-6 : angle 2.11345 / 1.21 ( 3) link_BETA1-4 : bond 0.00875 / 0.58 ( 10) link_BETA1-4 : angle 3.23474 / 2.05 ( 30) link_NAG-ASN : bond 0.01191 / 0.73 ( 10) link_NAG-ASN : angle 4.39723 / 2.93 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1092.10 seconds wall clock time: 19 minutes 23.52 seconds (1163.52 seconds total)