Starting phenix.real_space_refine (version: dev) on Sat Feb 18 05:00:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/02_2023/6djp_7939.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/02_2023/6djp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/02_2023/6djp_7939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/02_2023/6djp_7939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/02_2023/6djp_7939.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djp_7939/02_2023/6djp_7939.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 3.71 Conformation dependent library (CDL) restraints added in 1.6 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: 0.76 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: 2.66 Time building geometry restraints manager: 3.65 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=" C4 NAG G 2 " pdb=" O4 NAG G 2 " ideal model delta sigma weight residual 1.423 1.463 -0.040 1.00e-02 1.00e+04 1.58e+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=" C3 NAG G 2 " pdb=" C4 NAG G 2 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.00e-02 1.00e+04 1.45e+01 ... (remaining 7357 not shown) Histogram of bond angle deviations from ideal: 99.17 - 105.98: 331 105.98 - 112.80: 3672 112.80 - 119.62: 2336 119.62 - 126.43: 3863 126.43 - 133.25: 57 Bond angle restraints: 10259 Sorted by residual: angle pdb=" N ARG F 61 " pdb=" CA ARG F 61 " pdb=" C ARG F 61 " ideal model delta sigma weight residual 114.56 102.74 11.82 1.27e+00 6.20e-01 8.66e+01 angle pdb=" C MET A 400 " pdb=" N PRO A 401 " pdb=" CA PRO A 401 " ideal model delta sigma weight residual 119.66 126.19 -6.53 7.30e-01 1.88e+00 8.01e+01 angle pdb=" N TYR F 32 " pdb=" CA TYR F 32 " pdb=" C TYR F 32 " ideal model delta sigma weight residual 108.60 121.42 -12.82 1.46e+00 4.69e-01 7.71e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 128.35 -8.79 1.02e+00 9.61e-01 7.43e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.33 -8.77 1.02e+00 9.61e-01 7.40e+01 ... (remaining 10254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.89: 4175 9.89 - 19.79: 112 19.79 - 29.68: 8 29.68 - 39.57: 1 39.57 - 49.46: 2 Dihedral angle restraints: 4298 sinusoidal: 364 harmonic: 3934 Sorted by residual: dihedral pdb=" CA ASN C 61 " pdb=" C ASN C 61 " pdb=" N PRO C 62 " pdb=" CA PRO C 62 " ideal model delta harmonic sigma weight residual -180.00 -163.68 -16.32 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLY A 173 " pdb=" C GLY A 173 " pdb=" N PRO A 174 " pdb=" CA PRO A 174 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" N ASN A 524 " pdb=" CA ASN A 524 " pdb=" CB ASN A 524 " pdb=" CG ASN A 524 " ideal model delta sinusoidal sigma weight residual -60.00 -109.46 49.46 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 4295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1017 0.075 - 0.150: 302 0.150 - 0.225: 55 0.225 - 0.300: 11 0.300 - 0.376: 4 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 2.440 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 2.440 ... (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 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 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. 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: 1.000 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: 0.000 Extract box with map and model: 3.990 Check model and map are aligned: 0.110 Process input model: 25.190 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.089 7362 Z= 0.847 Angle : 1.996 17.240 10259 Z= 1.372 Chirality : 0.076 0.376 1389 Planarity : 0.009 0.042 1476 Dihedral : 5.342 49.465 1750 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.861 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0738 time to fit residues: 5.5876 Evaluate side-chains 30 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0514 ------------------------------------------------------------------------------- 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: 10.0000 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 55 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.0570 chunk 123 optimal weight: 2.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 7362 Z= 0.243 Angle : 0.671 13.860 10259 Z= 0.374 Chirality : 0.050 0.289 1389 Planarity : 0.004 0.049 1476 Dihedral : 5.596 27.921 1544 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.00 % 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: -0.30 (0.22), residues: 1379 helix: -0.25 (0.53), residues: 97 sheet: 0.15 (0.22), residues: 495 loop : -0.34 (0.22), residues: 787 *********************** 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 fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.780 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0690 time to fit residues: 5.1256 Evaluate side-chains 31 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 30.0000 chunk 38 optimal weight: 0.0270 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 overall best weight: 5.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.147 7362 Z= 0.669 Angle : 1.208 17.010 10259 Z= 0.714 Chirality : 0.055 0.358 1389 Planarity : 0.008 0.076 1476 Dihedral : 9.899 48.779 1544 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.65 % Allowed : 12.04 % Favored : 87.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -2.32 (0.21), residues: 1379 helix: -2.33 (0.43), residues: 98 sheet: -0.62 (0.23), residues: 477 loop : -2.08 (0.21), residues: 804 *********************** 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 fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.809 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0729 time to fit residues: 5.1325 Evaluate side-chains 29 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.0570 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.6743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 7362 Z= 0.268 Angle : 0.689 12.935 10259 Z= 0.383 Chirality : 0.048 0.392 1389 Planarity : 0.005 0.043 1476 Dihedral : 6.912 51.378 1544 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.22), residues: 1379 helix: -0.66 (0.55), residues: 95 sheet: -0.53 (0.23), residues: 486 loop : -1.66 (0.22), residues: 798 *********************** 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 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.859 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0696 time to fit residues: 4.8277 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.9456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.262 7362 Z= 0.973 Angle : 1.499 22.412 10259 Z= 0.899 Chirality : 0.065 0.394 1389 Planarity : 0.011 0.068 1476 Dihedral : 12.202 47.356 1544 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 37.03 Ramachandran Plot: Outliers : 2.54 % Allowed : 20.74 % Favored : 76.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 4.84 % Twisted General : 2.27 % 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: -4.31 (0.20), residues: 1379 helix: -3.93 (0.34), residues: 80 sheet: -1.49 (0.26), residues: 381 loop : -3.64 (0.17), residues: 918 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.857 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0706 time to fit residues: 4.9573 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.8746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 7362 Z= 0.256 Angle : 0.744 14.013 10259 Z= 0.419 Chirality : 0.050 0.432 1389 Planarity : 0.006 0.050 1476 Dihedral : 8.048 56.958 1544 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.82 % Favored : 88.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.21), residues: 1379 helix: -1.82 (0.45), residues: 86 sheet: -1.52 (0.24), residues: 447 loop : -2.93 (0.19), residues: 846 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.932 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0749 time to fit residues: 5.0300 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.9480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.197 7362 Z= 0.577 Angle : 0.997 16.351 10259 Z= 0.577 Chirality : 0.053 0.385 1389 Planarity : 0.007 0.052 1476 Dihedral : 9.323 47.344 1544 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 21.25 % Favored : 78.46 % Rotamer Outliers : 0.00 % 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: -4.08 (0.20), residues: 1379 helix: -2.70 (0.41), residues: 85 sheet: -1.76 (0.24), residues: 408 loop : -3.39 (0.18), residues: 886 *********************** 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 fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.711 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0648 time to fit residues: 4.4597 Evaluate side-chains 28 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.9769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.158 7362 Z= 0.469 Angle : 0.882 15.239 10259 Z= 0.507 Chirality : 0.051 0.430 1389 Planarity : 0.007 0.052 1476 Dihedral : 8.756 54.952 1544 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.65 % Favored : 80.35 % Rotamer Outliers : 0.00 % 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: -4.16 (0.20), residues: 1379 helix: -2.51 (0.42), residues: 86 sheet: -1.77 (0.25), residues: 403 loop : -3.49 (0.18), residues: 890 *********************** 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 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.847 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0693 time to fit residues: 4.6041 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 1.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.268 7362 Z= 0.686 Angle : 1.119 18.390 10259 Z= 0.655 Chirality : 0.055 0.428 1389 Planarity : 0.008 0.062 1476 Dihedral : 10.342 45.479 1544 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 25.38 % Favored : 74.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 1.28 % 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: -4.81 (0.19), residues: 1379 helix: -3.46 (0.34), residues: 85 sheet: -2.16 (0.25), residues: 389 loop : -3.92 (0.17), residues: 905 *********************** 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 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.833 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0718 time to fit residues: 4.8442 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 0.0870 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 114 optimal weight: 0.1980 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 1.0124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 7362 Z= 0.245 Angle : 0.696 14.096 10259 Z= 0.391 Chirality : 0.050 0.458 1389 Planarity : 0.006 0.056 1476 Dihedral : 7.581 57.301 1544 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.39 % Favored : 88.47 % Rotamer Outliers : 0.00 % 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: -3.99 (0.21), residues: 1379 helix: -1.26 (0.50), residues: 94 sheet: -2.11 (0.24), residues: 450 loop : -3.28 (0.19), residues: 835 ********************** 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 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.902 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0740 time to fit residues: 4.9311 Evaluate side-chains 27 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 6 optimal weight: 0.0050 overall best weight: 4.4002 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.079563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065281 restraints weight = 44810.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065694 restraints weight = 37328.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066337 restraints weight = 31438.842| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 1.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.208 7362 Z= 0.571 Angle : 0.964 17.190 10259 Z= 0.557 Chirality : 0.052 0.436 1389 Planarity : 0.007 0.054 1476 Dihedral : 9.121 51.784 1544 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 24.80 % Favored : 74.84 % Rotamer Outliers : 0.00 % 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: -4.58 (0.20), residues: 1379 helix: -2.53 (0.41), residues: 90 sheet: -2.32 (0.24), residues: 404 loop : -3.67 (0.18), residues: 885 =============================================================================== Job complete usr+sys time: 1166.10 seconds wall clock time: 21 minutes 57.86 seconds (1317.86 seconds total)