Starting phenix.real_space_refine on Fri Aug 22 20:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djp_7939/08_2025/6djp_7939.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djp_7939/08_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_7939/08_2025/6djp_7939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djp_7939/08_2025/6djp_7939.map" model { file = "/net/cci-nas-00/data/ceres_data/6djp_7939/08_2025/6djp_7939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djp_7939/08_2025/6djp_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-2.0-5787/lib/python3.9/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 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: 2.21, per 1000 atoms: 0.30 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: 0.88 Conformation dependent library (CDL) restraints added in 511.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 1.33 Time building geometry restraints manager: 1.11 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: 1.100 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01193 ( 7362) covalent geometry : angle 2.00986 (10259) hydrogen bonds : bond 0.16264 ( 369) hydrogen bonds : angle 9.33679 ( 939) link_ALPHA1-3 : bond 0.04582 ( 1) link_ALPHA1-3 : angle 3.12491 ( 3) 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_NAG-ASN : bond 0.03097 ( 10) link_NAG-ASN : angle 1.95909 ( 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 : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0334 time to fit residues: 2.3803 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 : 0.252 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092782 restraints weight = 43912.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092981 restraints weight = 36895.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093669 restraints weight = 34505.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094324 restraints weight = 29388.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094674 restraints weight = 25061.251| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7385 Z= 0.153 Angle : 0.750 13.385 10328 Z= 0.370 Chirality : 0.051 0.329 1389 Planarity : 0.004 0.050 1476 Dihedral : 8.575 78.740 1859 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.98 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 aren not related in a simple way. whole: -0.21 (0.22), residues: 1379 helix: -0.16 (0.53), residues: 97 sheet: 0.14 (0.22), residues: 503 loop : -0.23 (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 covalent geometry : bond 0.00268 ( 7362) covalent geometry : angle 0.70105 (10259) hydrogen bonds : bond 0.03530 ( 369) hydrogen bonds : angle 6.70415 ( 939) link_ALPHA1-3 : bond 0.01259 ( 1) link_ALPHA1-3 : angle 2.70758 ( 3) link_ALPHA1-4 : bond 0.00487 ( 1) link_ALPHA1-4 : angle 1.81593 ( 3) link_ALPHA1-6 : bond 0.00012 ( 1) link_ALPHA1-6 : angle 3.14344 ( 3) link_BETA1-4 : bond 0.00899 ( 10) link_BETA1-4 : angle 3.79624 ( 30) link_NAG-ASN : bond 0.00547 ( 10) link_NAG-ASN : angle 2.98582 ( 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 : 0.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0292 time to fit residues: 1.9866 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 : 0.255 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 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: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.093043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075666 restraints weight = 43188.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076527 restraints weight = 35332.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077255 restraints weight = 30017.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077733 restraints weight = 26275.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078185 restraints weight = 23646.880| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 7385 Z= 0.296 Angle : 0.955 13.012 10328 Z= 0.501 Chirality : 0.050 0.224 1389 Planarity : 0.006 0.047 1476 Dihedral : 9.585 68.478 1859 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % 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 aren not related in a simple way. whole: -1.22 (0.22), residues: 1379 helix: -0.82 (0.50), residues: 98 sheet: -0.19 (0.22), residues: 508 loop : -1.23 (0.22), residues: 773 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 covalent geometry : bond 0.00490 ( 7362) covalent geometry : angle 0.90965 (10259) hydrogen bonds : bond 0.05903 ( 369) hydrogen bonds : angle 8.13204 ( 939) link_ALPHA1-3 : bond 0.00796 ( 1) link_ALPHA1-3 : angle 4.35688 ( 3) link_ALPHA1-4 : bond 0.00712 ( 1) link_ALPHA1-4 : angle 2.35664 ( 3) link_ALPHA1-6 : bond 0.00140 ( 1) link_ALPHA1-6 : angle 2.62320 ( 3) link_BETA1-4 : bond 0.01236 ( 10) link_BETA1-4 : angle 3.96068 ( 30) link_NAG-ASN : bond 0.01427 ( 10) link_NAG-ASN : angle 3.51056 ( 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 : 0.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0328 time to fit residues: 2.1653 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 : 0.303 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.093572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076112 restraints weight = 43482.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077070 restraints weight = 35210.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077773 restraints weight = 29534.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078402 restraints weight = 25689.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078951 restraints weight = 22784.545| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7385 Z= 0.179 Angle : 0.701 11.263 10328 Z= 0.351 Chirality : 0.048 0.270 1389 Planarity : 0.005 0.041 1476 Dihedral : 7.994 59.213 1859 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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 aren not related in a simple way. whole: -1.08 (0.23), residues: 1379 helix: -0.26 (0.53), residues: 105 sheet: -0.23 (0.22), residues: 507 loop : -1.10 (0.23), residues: 767 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 covalent geometry : bond 0.00304 ( 7362) covalent geometry : angle 0.66917 (10259) hydrogen bonds : bond 0.03622 ( 369) hydrogen bonds : angle 6.86670 ( 939) link_ALPHA1-3 : bond 0.01582 ( 1) link_ALPHA1-3 : angle 2.22178 ( 3) link_ALPHA1-4 : bond 0.00237 ( 1) link_ALPHA1-4 : angle 1.64632 ( 3) link_ALPHA1-6 : bond 0.00601 ( 1) link_ALPHA1-6 : angle 2.40878 ( 3) link_BETA1-4 : bond 0.00632 ( 10) link_BETA1-4 : angle 2.86804 ( 30) link_NAG-ASN : bond 0.00552 ( 10) link_NAG-ASN : angle 2.52692 ( 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 : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0327 time to fit residues: 1.9730 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 : 0.205 ------------------------------------------------------------------------------- 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: 0.0670 chunk 74 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 54 optimal weight: 0.0870 chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.0370 chunk 127 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9976 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.093560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075955 restraints weight = 42680.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076942 restraints weight = 34314.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.077729 restraints weight = 28661.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078441 restraints weight = 24805.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078950 restraints weight = 22134.811| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7385 Z= 0.135 Angle : 0.658 13.311 10328 Z= 0.318 Chirality : 0.047 0.201 1389 Planarity : 0.004 0.044 1476 Dihedral : 7.324 55.756 1859 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % 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 aren not related in a simple way. whole: -0.90 (0.23), residues: 1379 helix: 0.53 (0.58), residues: 99 sheet: -0.18 (0.23), residues: 503 loop : -1.02 (0.23), residues: 777 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 covalent geometry : bond 0.00234 ( 7362) covalent geometry : angle 0.61187 (10259) hydrogen bonds : bond 0.03128 ( 369) hydrogen bonds : angle 6.35908 ( 939) link_ALPHA1-3 : bond 0.01213 ( 1) link_ALPHA1-3 : angle 3.07483 ( 3) link_ALPHA1-4 : bond 0.00230 ( 1) link_ALPHA1-4 : angle 1.86062 ( 3) link_ALPHA1-6 : bond 0.00344 ( 1) link_ALPHA1-6 : angle 2.21752 ( 3) link_BETA1-4 : bond 0.00808 ( 10) link_BETA1-4 : angle 2.74307 ( 30) link_NAG-ASN : bond 0.00789 ( 10) link_NAG-ASN : angle 3.39924 ( 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 29 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0319 time to fit residues: 2.0885 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 : 0.313 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 104 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.087945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070835 restraints weight = 43974.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071718 restraints weight = 35593.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.072375 restraints weight = 29789.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072965 restraints weight = 26093.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073505 restraints weight = 23243.264| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 7385 Z= 0.265 Angle : 0.865 11.499 10328 Z= 0.441 Chirality : 0.049 0.311 1389 Planarity : 0.005 0.043 1476 Dihedral : 8.854 55.414 1859 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % 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 aren not related in a simple way. whole: -1.85 (0.23), residues: 1379 helix: -0.48 (0.53), residues: 98 sheet: -0.84 (0.24), residues: 489 loop : -1.59 (0.22), residues: 792 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 covalent geometry : bond 0.00442 ( 7362) covalent geometry : angle 0.81632 (10259) hydrogen bonds : bond 0.05022 ( 369) hydrogen bonds : angle 8.12463 ( 939) link_ALPHA1-3 : bond 0.01289 ( 1) link_ALPHA1-3 : angle 3.06960 ( 3) link_ALPHA1-4 : bond 0.00906 ( 1) link_ALPHA1-4 : angle 2.15580 ( 3) link_ALPHA1-6 : bond 0.00047 ( 1) link_ALPHA1-6 : angle 2.88447 ( 3) link_BETA1-4 : bond 0.00788 ( 10) link_BETA1-4 : angle 3.53571 ( 30) link_NAG-ASN : bond 0.01120 ( 10) link_NAG-ASN : angle 3.89237 ( 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 27 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0342 time to fit residues: 2.1495 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 : 0.179 ------------------------------------------------------------------------------- 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: 10.0000 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 57 optimal weight: 0.0570 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 overall best weight: 2.6904 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.069930 restraints weight = 44377.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070832 restraints weight = 35579.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071505 restraints weight = 29659.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072081 restraints weight = 25631.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072598 restraints weight = 22743.957| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.8407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 7385 Z= 0.266 Angle : 0.832 11.979 10328 Z= 0.428 Chirality : 0.048 0.266 1389 Planarity : 0.005 0.052 1476 Dihedral : 8.845 51.583 1859 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % 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 aren not related in a simple way. whole: -2.34 (0.22), residues: 1379 helix: -0.83 (0.51), residues: 98 sheet: -1.14 (0.24), residues: 481 loop : -1.95 (0.22), 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 covalent geometry : bond 0.00449 ( 7362) covalent geometry : angle 0.79329 (10259) hydrogen bonds : bond 0.04644 ( 369) hydrogen bonds : angle 8.15272 ( 939) link_ALPHA1-3 : bond 0.01305 ( 1) link_ALPHA1-3 : angle 3.09085 ( 3) link_ALPHA1-4 : bond 0.00534 ( 1) link_ALPHA1-4 : angle 1.83864 ( 3) link_ALPHA1-6 : bond 0.00197 ( 1) link_ALPHA1-6 : angle 2.21384 ( 3) link_BETA1-4 : bond 0.00759 ( 10) link_BETA1-4 : angle 2.99244 ( 30) link_NAG-ASN : bond 0.01038 ( 10) link_NAG-ASN : angle 3.48741 ( 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 29 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0335 time to fit residues: 2.2042 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 : 0.271 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.085644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070298 restraints weight = 44145.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.070755 restraints weight = 34785.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071377 restraints weight = 29723.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.071873 restraints weight = 24754.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.072376 restraints weight = 21520.016| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 7385 Z= 0.244 Angle : 0.809 12.336 10328 Z= 0.412 Chirality : 0.048 0.303 1389 Planarity : 0.005 0.055 1476 Dihedral : 8.886 58.018 1859 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.26 % Favored : 87.67 % 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 aren not related in a simple way. whole: -2.52 (0.22), residues: 1379 helix: -0.84 (0.49), residues: 101 sheet: -1.19 (0.24), residues: 459 loop : -2.14 (0.21), residues: 819 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 covalent geometry : bond 0.00413 ( 7362) covalent geometry : angle 0.76904 (10259) hydrogen bonds : bond 0.04522 ( 369) hydrogen bonds : angle 8.21863 ( 939) link_ALPHA1-3 : bond 0.01483 ( 1) link_ALPHA1-3 : angle 2.51770 ( 3) link_ALPHA1-4 : bond 0.00571 ( 1) link_ALPHA1-4 : angle 1.97732 ( 3) link_ALPHA1-6 : bond 0.00541 ( 1) link_ALPHA1-6 : angle 3.03541 ( 3) link_BETA1-4 : bond 0.00733 ( 10) link_BETA1-4 : angle 2.98991 ( 30) link_NAG-ASN : bond 0.00992 ( 10) link_NAG-ASN : angle 3.52507 ( 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 29 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0298 time to fit residues: 2.0200 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.12 > 50: distance: 9 - 130: 34.688 distance: 60 - 125: 34.924 distance: 63 - 122: 37.256 distance: 70 - 115: 36.686 distance: 73 - 112: 33.964 distance: 79 - 105: 37.138 distance: 82 - 102: 33.895 distance: 94 - 97: 34.039 distance: 98 - 101: 40.297 distance: 99 - 100: 56.263 distance: 102 - 103: 57.254 distance: 104 - 105: 56.606 distance: 104 - 107: 8.850 distance: 107 - 108: 42.208 distance: 108 - 109: 40.536 distance: 109 - 110: 39.329 distance: 109 - 112: 56.316 distance: 112 - 113: 41.157 distance: 113 - 114: 53.748 distance: 113 - 116: 53.941 distance: 114 - 115: 52.279 distance: 114 - 117: 4.747 distance: 117 - 118: 5.093 distance: 118 - 121: 49.287 distance: 119 - 120: 41.043 distance: 119 - 122: 69.029 distance: 123 - 124: 18.737 distance: 123 - 126: 56.292 distance: 124 - 125: 40.389 distance: 124 - 127: 40.907 distance: 127 - 128: 6.899 distance: 128 - 129: 22.262 distance: 128 - 131: 48.382 distance: 129 - 130: 40.666 distance: 132 - 133: 39.526 distance: 133 - 134: 40.482 distance: 133 - 136: 40.113 distance: 134 - 135: 39.286 distance: 134 - 137: 13.981 distance: 137 - 138: 50.734 distance: 138 - 139: 42.124 distance: 138 - 141: 40.938 distance: 139 - 140: 55.858 distance: 142 - 148: 40.200 distance: 143 - 144: 42.572 distance: 143 - 146: 40.081 distance: 144 - 145: 23.909 distance: 144 - 149: 28.474 distance: 146 - 147: 39.266 distance: 147 - 148: 39.320