Starting phenix.real_space_refine on Mon Apr 28 12:55:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djp_7939/04_2025/6djp_7939.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djp_7939/04_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_7939/04_2025/6djp_7939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djp_7939/04_2025/6djp_7939.map" model { file = "/net/cci-nas-00/data/ceres_data/6djp_7939/04_2025/6djp_7939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djp_7939/04_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-5669/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: 5.34, per 1000 atoms: 0.73 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 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: 2.73 Time building geometry restraints manager: 2.77 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: 0.690 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.130 Find NCS groups from input model: 0.130 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- 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 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 : 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 Details of bonding type rmsd link_NAG-ASN : bond 0.03097 ( 10) link_NAG-ASN : angle 1.95909 ( 30) link_ALPHA1-4 : bond 0.04724 ( 1) link_ALPHA1-4 : angle 3.55752 ( 3) link_ALPHA1-6 : bond 0.02959 ( 1) link_ALPHA1-6 : angle 2.31754 ( 3) link_BETA1-4 : bond 0.03712 ( 10) link_BETA1-4 : angle 4.44525 ( 30) link_ALPHA1-3 : bond 0.04582 ( 1) link_ALPHA1-3 : angle 3.12491 ( 3) hydrogen bonds : bond 0.16264 ( 369) hydrogen bonds : angle 9.33679 ( 939) covalent geometry : bond 0.01193 ( 7362) covalent geometry : angle 2.00986 (10259) *********************** 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 : 0.764 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0686 time to fit residues: 5.2181 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 : 0.760 ------------------------------------------------------------------------------- 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 = 0.091766 restraints weight = 43182.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092304 restraints weight = 37397.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093081 restraints weight = 32707.885| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 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 7385 Z= 0.169 Angle : 0.766 13.713 10328 Z= 0.378 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 10) link_NAG-ASN : angle 2.97746 ( 30) link_ALPHA1-4 : bond 0.00457 ( 1) link_ALPHA1-4 : angle 1.77826 ( 3) link_ALPHA1-6 : bond 0.00018 ( 1) link_ALPHA1-6 : angle 3.01430 ( 3) link_BETA1-4 : bond 0.00958 ( 10) link_BETA1-4 : angle 3.96404 ( 30) link_ALPHA1-3 : bond 0.01186 ( 1) link_ALPHA1-3 : angle 2.58197 ( 3) hydrogen bonds : bond 0.03758 ( 369) hydrogen bonds : angle 6.78470 ( 939) covalent geometry : bond 0.00291 ( 7362) covalent geometry : angle 0.71647 (10259) *********************** 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 : 0.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0654 time to fit residues: 4.8745 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 : 0.756 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.095802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079168 restraints weight = 43118.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.079500 restraints weight = 35833.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080111 restraints weight = 32404.571| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 7385 Z= 0.235 Angle : 0.805 12.046 10328 Z= 0.415 Chirality : 0.049 0.255 1389 Planarity : 0.005 0.049 1476 Dihedral : 8.506 66.726 1859 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % 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: -0.82 (0.22), residues: 1379 helix: -0.53 (0.50), residues: 105 sheet: 0.03 (0.23), residues: 508 loop : -0.93 (0.22), residues: 766 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 10) link_NAG-ASN : angle 2.63443 ( 30) link_ALPHA1-4 : bond 0.00434 ( 1) link_ALPHA1-4 : angle 2.20288 ( 3) link_ALPHA1-6 : bond 0.00452 ( 1) link_ALPHA1-6 : angle 2.18615 ( 3) link_BETA1-4 : bond 0.01155 ( 10) link_BETA1-4 : angle 3.24629 ( 30) link_ALPHA1-3 : bond 0.01012 ( 1) link_ALPHA1-3 : angle 4.43205 ( 3) hydrogen bonds : bond 0.04670 ( 369) hydrogen bonds : angle 7.06729 ( 939) covalent geometry : bond 0.00402 ( 7362) covalent geometry : angle 0.76961 (10259) *********************** 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 : 0.815 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0671 time to fit residues: 4.6659 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 : 0.729 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 0.0170 chunk 131 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.087061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071316 restraints weight = 44048.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071897 restraints weight = 36041.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.072164 restraints weight = 31784.370| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 7385 Z= 0.376 Angle : 1.070 14.088 10328 Z= 0.564 Chirality : 0.053 0.300 1389 Planarity : 0.007 0.053 1476 Dihedral : 10.123 57.735 1859 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.30 % Favored : 89.63 % 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 : 0.23 % 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: -2.02 (0.22), residues: 1379 helix: -1.20 (0.52), residues: 81 sheet: -0.72 (0.23), residues: 480 loop : -1.79 (0.21), residues: 818 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01206 ( 10) link_NAG-ASN : angle 4.50097 ( 30) link_ALPHA1-4 : bond 0.00808 ( 1) link_ALPHA1-4 : angle 2.15867 ( 3) link_ALPHA1-6 : bond 0.00015 ( 1) link_ALPHA1-6 : angle 3.40677 ( 3) link_BETA1-4 : bond 0.01026 ( 10) link_BETA1-4 : angle 4.29767 ( 30) link_ALPHA1-3 : bond 0.00783 ( 1) link_ALPHA1-3 : angle 4.00619 ( 3) hydrogen bonds : bond 0.06166 ( 369) hydrogen bonds : angle 9.10833 ( 939) covalent geometry : bond 0.00609 ( 7362) covalent geometry : angle 1.01440 (10259) *********************** 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 27 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.766 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0662 time to fit residues: 4.4421 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 : 0.757 ------------------------------------------------------------------------------- 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: 20.0000 chunk 35 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 7 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.087759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.071873 restraints weight = 43426.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.072433 restraints weight = 35773.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072830 restraints weight = 31147.596| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 7385 Z= 0.263 Angle : 0.868 18.247 10328 Z= 0.437 Chirality : 0.050 0.378 1389 Planarity : 0.006 0.052 1476 Dihedral : 9.157 59.005 1859 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % 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 : 0.08 % 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: -2.14 (0.22), residues: 1379 helix: -0.53 (0.55), residues: 86 sheet: -1.03 (0.23), residues: 490 loop : -1.81 (0.22), residues: 803 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01322 ( 10) link_NAG-ASN : angle 4.77512 ( 30) link_ALPHA1-4 : bond 0.00606 ( 1) link_ALPHA1-4 : angle 1.84075 ( 3) link_ALPHA1-6 : bond 0.00337 ( 1) link_ALPHA1-6 : angle 2.70837 ( 3) link_BETA1-4 : bond 0.00837 ( 10) link_BETA1-4 : angle 3.18507 ( 30) link_ALPHA1-3 : bond 0.01235 ( 1) link_ALPHA1-3 : angle 3.14873 ( 3) hydrogen bonds : bond 0.04792 ( 369) hydrogen bonds : angle 8.30710 ( 939) covalent geometry : bond 0.00450 ( 7362) covalent geometry : angle 0.81001 (10259) *********************** 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 : 0.845 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0666 time to fit residues: 4.5801 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 : 0.830 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 131 optimal weight: 0.0870 chunk 66 optimal weight: 7.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.082814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.067412 restraints weight = 44699.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.068120 restraints weight = 36427.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.068500 restraints weight = 30205.769| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.8875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 7385 Z= 0.450 Angle : 1.153 15.982 10328 Z= 0.601 Chirality : 0.054 0.361 1389 Planarity : 0.007 0.057 1476 Dihedral : 11.063 56.319 1859 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.62 % Favored : 82.31 % 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 : 0.38 % 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: -3.16 (0.21), residues: 1379 helix: -2.11 (0.45), residues: 86 sheet: -1.32 (0.26), residues: 393 loop : -2.62 (0.19), residues: 900 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01602 ( 10) link_NAG-ASN : angle 4.89654 ( 30) link_ALPHA1-4 : bond 0.01214 ( 1) link_ALPHA1-4 : angle 2.26953 ( 3) link_ALPHA1-6 : bond 0.00275 ( 1) link_ALPHA1-6 : angle 3.33528 ( 3) link_BETA1-4 : bond 0.01290 ( 10) link_BETA1-4 : angle 4.21117 ( 30) link_ALPHA1-3 : bond 0.00897 ( 1) link_ALPHA1-3 : angle 3.91112 ( 3) hydrogen bonds : bond 0.07002 ( 369) hydrogen bonds : angle 10.14904 ( 939) covalent geometry : bond 0.00749 ( 7362) covalent geometry : angle 1.09833 (10259) *********************** 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 27 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.773 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0685 time to fit residues: 4.6262 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 : 0.767 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.083481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.067377 restraints weight = 44119.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.068118 restraints weight = 35828.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068739 restraints weight = 30377.573| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.9164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 7385 Z= 0.329 Angle : 0.964 17.148 10328 Z= 0.496 Chirality : 0.050 0.326 1389 Planarity : 0.006 0.050 1476 Dihedral : 10.394 55.127 1859 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.16 % Favored : 84.84 % 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 : 0.38 % 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: -1.88 (0.48), residues: 92 sheet: -1.38 (0.26), residues: 397 loop : -2.80 (0.19), residues: 890 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01236 ( 10) link_NAG-ASN : angle 4.07571 ( 30) link_ALPHA1-4 : bond 0.00761 ( 1) link_ALPHA1-4 : angle 1.88858 ( 3) link_ALPHA1-6 : bond 0.00128 ( 1) link_ALPHA1-6 : angle 2.77789 ( 3) link_BETA1-4 : bond 0.00839 ( 10) link_BETA1-4 : angle 3.39733 ( 30) link_ALPHA1-3 : bond 0.01212 ( 1) link_ALPHA1-3 : angle 3.25643 ( 3) hydrogen bonds : bond 0.05676 ( 369) hydrogen bonds : angle 9.46606 ( 939) covalent geometry : bond 0.00559 ( 7362) covalent geometry : angle 0.92042 (10259) *********************** 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 : 0.791 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0708 time to fit residues: 4.7843 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 : 0.850 ------------------------------------------------------------------------------- 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: 0.4980 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.082394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067802 restraints weight = 45035.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068306 restraints weight = 35728.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.068760 restraints weight = 30487.513| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.9893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 7385 Z= 0.337 Angle : 0.981 15.634 10328 Z= 0.507 Chirality : 0.051 0.355 1389 Planarity : 0.006 0.053 1476 Dihedral : 10.423 59.579 1859 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 19.43 % Favored : 80.49 % 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: -3.67 (0.21), residues: 1379 helix: -2.10 (0.45), residues: 91 sheet: -1.76 (0.25), residues: 399 loop : -2.97 (0.19), residues: 889 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01181 ( 10) link_NAG-ASN : angle 4.11433 ( 30) link_ALPHA1-4 : bond 0.00827 ( 1) link_ALPHA1-4 : angle 2.04683 ( 3) link_ALPHA1-6 : bond 0.00474 ( 1) link_ALPHA1-6 : angle 2.96952 ( 3) link_BETA1-4 : bond 0.00912 ( 10) link_BETA1-4 : angle 3.48598 ( 30) link_ALPHA1-3 : bond 0.01105 ( 1) link_ALPHA1-3 : angle 2.21065 ( 3) hydrogen bonds : bond 0.05824 ( 369) hydrogen bonds : angle 9.58978 ( 939) covalent geometry : bond 0.00572 ( 7362) covalent geometry : angle 0.93714 (10259) *********************** 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 : 0.772 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0661 time to fit residues: 4.5918 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 : 0.763 ------------------------------------------------------------------------------- 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: 2.9990 chunk 109 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.083152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068550 restraints weight = 45012.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069144 restraints weight = 35692.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069462 restraints weight = 30525.316| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 1.0024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 7385 Z= 0.282 Angle : 0.898 16.709 10328 Z= 0.458 Chirality : 0.049 0.318 1389 Planarity : 0.006 0.047 1476 Dihedral : 9.934 59.843 1859 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.74 % Favored : 84.19 % 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: -3.65 (0.21), residues: 1379 helix: -1.52 (0.49), residues: 85 sheet: -1.78 (0.25), residues: 407 loop : -3.01 (0.19), 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01011 ( 10) link_NAG-ASN : angle 3.83278 ( 30) link_ALPHA1-4 : bond 0.00492 ( 1) link_ALPHA1-4 : angle 1.87953 ( 3) link_ALPHA1-6 : bond 0.00629 ( 1) link_ALPHA1-6 : angle 2.56716 ( 3) link_BETA1-4 : bond 0.00771 ( 10) link_BETA1-4 : angle 2.98896 ( 30) link_ALPHA1-3 : bond 0.00893 ( 1) link_ALPHA1-3 : angle 1.62366 ( 3) hydrogen bonds : bond 0.05171 ( 369) hydrogen bonds : angle 9.19568 ( 939) covalent geometry : bond 0.00480 ( 7362) covalent geometry : angle 0.85928 (10259) *********************** 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 : 0.764 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0663 time to fit residues: 4.5590 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 : 0.755 ------------------------------------------------------------------------------- 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: 7.9990 chunk 127 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.081271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066634 restraints weight = 45799.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067157 restraints weight = 37045.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.067709 restraints weight = 31085.051| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 1.0525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 7385 Z= 0.353 Angle : 1.008 17.001 10328 Z= 0.522 Chirality : 0.051 0.346 1389 Planarity : 0.006 0.051 1476 Dihedral : 10.518 58.946 1859 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 21.46 % Favored : 78.39 % 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: -4.01 (0.21), residues: 1379 helix: -2.19 (0.46), residues: 91 sheet: -1.97 (0.25), residues: 390 loop : -3.24 (0.19), residues: 898 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01166 ( 10) link_NAG-ASN : angle 4.24577 ( 30) link_ALPHA1-4 : bond 0.00704 ( 1) link_ALPHA1-4 : angle 2.16742 ( 3) link_ALPHA1-6 : bond 0.00740 ( 1) link_ALPHA1-6 : angle 3.28771 ( 3) link_BETA1-4 : bond 0.00994 ( 10) link_BETA1-4 : angle 3.46272 ( 30) link_ALPHA1-3 : bond 0.01053 ( 1) link_ALPHA1-3 : angle 1.55539 ( 3) hydrogen bonds : bond 0.06089 ( 369) hydrogen bonds : angle 9.93600 ( 939) covalent geometry : bond 0.00597 ( 7362) covalent geometry : angle 0.96393 (10259) ********************** 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 : 0.879 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0712 time to fit residues: 4.9682 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 : 0.859 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 0.0870 chunk 99 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 0.0570 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.4282 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.083046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068431 restraints weight = 44412.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069075 restraints weight = 35879.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.069603 restraints weight = 29084.255| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 1.0481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 7385 Z= 0.254 Angle : 0.869 15.219 10328 Z= 0.441 Chirality : 0.049 0.314 1389 Planarity : 0.006 0.048 1476 Dihedral : 9.708 57.771 1859 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.59 % Favored : 84.34 % 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: -3.87 (0.21), residues: 1379 helix: -1.42 (0.51), residues: 85 sheet: -2.13 (0.24), residues: 427 loop : -3.08 (0.20), residues: 867 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00903 ( 10) link_NAG-ASN : angle 3.76223 ( 30) link_ALPHA1-4 : bond 0.00258 ( 1) link_ALPHA1-4 : angle 1.95810 ( 3) link_ALPHA1-6 : bond 0.00987 ( 1) link_ALPHA1-6 : angle 2.76610 ( 3) link_BETA1-4 : bond 0.00738 ( 10) link_BETA1-4 : angle 2.86170 ( 30) link_ALPHA1-3 : bond 0.00829 ( 1) link_ALPHA1-3 : angle 1.26049 ( 3) hydrogen bonds : bond 0.04911 ( 369) hydrogen bonds : angle 9.14482 ( 939) covalent geometry : bond 0.00433 ( 7362) covalent geometry : angle 0.83118 (10259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.72 seconds wall clock time: 36 minutes 13.88 seconds (2173.88 seconds total)