Starting phenix.real_space_refine on Fri Sep 11 12:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ujb_20795/09_2026/6ujb_20795.cif" } resolution = 3.51 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= 0.003 sd= 0.060 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 43 5.16 5 C 5792 2.51 5 N 1549 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9193 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4387 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 564} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'ARG:plan': 5, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2812 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 898 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "D" 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: "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: 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: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.77, per 1000 atoms: 0.19 Number of scatterers: 9193 At special positions: 0 Unit cell: (72.63, 100.875, 165.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 43 16.00 Mg 1 11.99 O 1803 8.00 N 1549 7.00 C 5792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.02 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.06 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.05 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 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 ALPHA1-2 " MAN C 4 " - " MAN C 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2005 " - " ASN A 260 " " NAG B2005 " - " ASN B 360 " " NAG B2010 " - " ASN B 379 " " NAG C 1 " - " ASN A 266 " " NAG D 1 " - " ASN A 44 " " NAG G 1 " - " ASN B 191 " " NAG H 1 " - " ASN B 389 " " NAG I 1 " - " ASN B 414 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 280.0 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 13.6% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 366 through 370 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 122 Processing helix chain 'B' and resid 123 through 136 removed outlier: 3.519A pdb=" N VAL B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 130 " --> pdb=" O SER B 126 " (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 248 through 256 removed outlier: 3.791A pdb=" N SER B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.712A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 4.326A pdb=" N ARG E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 100 through 104 removed outlier: 4.313A pdb=" N ASP E 104 " --> pdb=" O TYR E 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.793A pdb=" N LEU F 89 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.200A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR A 412 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 423 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY A 410 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY A 425 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 408 " --> pdb=" O GLY A 425 " (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: 7.071A 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: 4.010A 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 164 removed outlier: 3.710A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.516A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 255 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 283 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 344 through 348 removed outlier: 6.441A pdb=" N ILE A 344 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 361 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA A 359 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 348 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 389 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.328A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 471 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 462 removed outlier: 7.328A pdb=" N LYS A 459 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.661A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 83 " --> pdb=" O HIS B 422 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB7, first strand: chain 'B' and resid 182 through 189 removed outlier: 5.298A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 299 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.414A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.508A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 345 hydrogen bonds defined for protein. 867 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: 1.70 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1827 1.32 - 1.45: 2418 1.45 - 1.58: 5059 1.58 - 1.71: 9 1.71 - 1.83: 66 Bond restraints: 9379 Sorted by residual: bond pdb=" CB HIS B 184 " pdb=" CG HIS B 184 " ideal model delta sigma weight residual 1.497 1.445 0.052 1.40e-02 5.10e+03 1.37e+01 bond pdb=" CB ASN B 332 " pdb=" CG ASN B 332 " ideal model delta sigma weight residual 1.516 1.430 0.086 2.50e-02 1.60e+03 1.17e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.455 -0.071 2.10e-02 2.27e+03 1.15e+01 bond pdb=" C5 NAG A2005 " pdb=" O5 NAG A2005 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 9374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.77: 12719 7.77 - 15.54: 5 15.54 - 23.30: 0 23.30 - 31.07: 0 31.07 - 38.84: 1 Bond angle restraints: 12725 Sorted by residual: angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 163.40 -38.84 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.17 -8.61 1.02e+00 9.61e-01 7.12e+01 angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 127.81 -8.25 1.02e+00 9.61e-01 6.54e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.41 -7.85 1.02e+00 9.61e-01 5.93e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.40 -7.84 1.02e+00 9.61e-01 5.91e+01 ... (remaining 12720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5262 17.94 - 35.87: 148 35.87 - 53.81: 32 53.81 - 71.74: 21 71.74 - 89.68: 11 Dihedral angle restraints: 5474 sinusoidal: 2084 harmonic: 3390 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual 93.00 40.72 52.28 1 1.00e+01 1.00e-02 3.73e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 94 " pdb=" CB CYS F 94 " ideal model delta sinusoidal sigma weight residual 93.00 52.10 40.90 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 5471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1000 0.071 - 0.141: 343 0.141 - 0.212: 61 0.212 - 0.283: 32 0.283 - 0.354: 18 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.44e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.07e+01 chirality pdb=" C1 MAN C 5 " pdb=" O2 MAN C 4 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 7.47e+00 ... (remaining 1451 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.12e-02 1.22e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.048 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 379 " -0.023 2.00e-02 2.50e+03 2.44e-02 7.46e+00 pdb=" CG ASN B 379 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 379 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 379 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B2010 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.021 2.00e-02 2.50e+03 2.26e-02 6.40e+00 pdb=" CG ASN A 44 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.028 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 25 2.41 - 3.03: 5542 3.03 - 3.65: 12893 3.65 - 4.28: 21698 4.28 - 4.90: 34934 Nonbonded interactions: 75092 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.782 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 1.955 2.170 nonbonded pdb=" OD2 ASP B 151 " pdb="CA CA B2001 " model vdw 2.095 2.510 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.099 2.510 nonbonded pdb=" OD1 ASP B 209 " pdb="CA CA B2001 " model vdw 2.104 2.510 ... (remaining 75087 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 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.950 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.015 0.086 9405 Z= 0.790 Angle : 1.455 38.841 12794 Z= 0.955 Chirality : 0.084 0.354 1454 Planarity : 0.006 0.027 1645 Dihedral : 10.926 89.680 3279 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.23), residues: 1170 helix: -1.33 (0.43), residues: 97 sheet: 1.03 (0.23), residues: 429 loop : 0.29 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 231 TYR 0.034 0.005 TYR A 254 PHE 0.021 0.004 PHE A 276 TRP 0.023 0.006 TRP A 179 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.01440 / 0.78 ( 9379) covalent geometry : angle 1.44549 / 0.96 (12725) SS BOND : bond 0.01432 / 0.69 ( 9) SS BOND : angle 1.85822 / 1.20 ( 18) hydrogen bonds : bond 0.16218 / 10.26 ( 331) hydrogen bonds : angle 8.74887 / 5.97 ( 867) link_ALPHA1-2 : bond 0.07545 / 3.97 ( 1) link_ALPHA1-2 : angle 3.73079 / 2.48 ( 3) link_ALPHA1-3 : bond 0.07384 / 3.89 ( 1) link_ALPHA1-3 : angle 3.21876 / 2.32 ( 3) link_ALPHA1-6 : bond 0.05592 / 2.94 ( 1) link_ALPHA1-6 : angle 3.04015 / 1.67 ( 3) link_BETA1-4 : bond 0.06287 / 3.42 ( 6) link_BETA1-4 : angle 3.32913 / 1.95 ( 18) link_NAG-ASN : bond 0.06410 / 3.37 ( 8) link_NAG-ASN : angle 2.20889 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7791 (t0) cc_final: 0.7577 (t0) REVERT: A 191 ILE cc_start: 0.8818 (mt) cc_final: 0.7931 (mt) REVERT: A 408 MET cc_start: 0.8061 (mtm) cc_final: 0.7859 (mtm) REVERT: B 117 MET cc_start: 0.9137 (mmm) cc_final: 0.8853 (mmm) REVERT: B 135 MET cc_start: 0.8005 (mmm) cc_final: 0.7788 (mmm) REVERT: E 43 LYS cc_start: 0.8263 (mttt) cc_final: 0.7989 (mppt) REVERT: E 50 ARG cc_start: 0.7998 (ptm-80) cc_final: 0.7746 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1174 time to fit residues: 27.5819 Evaluate side-chains 90 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 377 ASN B 166 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103726 restraints weight = 15239.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106550 restraints weight = 9050.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108335 restraints weight = 6468.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109527 restraints weight = 5160.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110172 restraints weight = 4424.020| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9405 Z= 0.181 Angle : 0.655 8.581 12794 Z= 0.341 Chirality : 0.048 0.169 1454 Planarity : 0.004 0.037 1645 Dihedral : 4.915 24.446 1268 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.61 % Allowed : 6.98 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1170 helix: -0.39 (0.49), residues: 96 sheet: 0.69 (0.23), residues: 457 loop : 0.28 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 164 TYR 0.016 0.002 TYR A 561 PHE 0.014 0.002 PHE B 306 TRP 0.011 0.002 TRP A 61 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 9379) covalent geometry : angle 0.63640 / 0.34 (12725) SS BOND : bond 0.00712 / 0.31 ( 9) SS BOND : angle 1.88121 / 0.76 ( 18) hydrogen bonds : bond 0.04078 / 2.57 ( 331) hydrogen bonds : angle 6.80235 / 4.69 ( 867) link_ALPHA1-2 : bond 0.00597 / 0.31 ( 1) link_ALPHA1-2 : angle 1.40597 / 1.12 ( 3) link_ALPHA1-3 : bond 0.01361 / 0.72 ( 1) link_ALPHA1-3 : angle 1.47988 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00822 / 0.43 ( 1) link_ALPHA1-6 : angle 1.44290 / 1.22 ( 3) link_BETA1-4 : bond 0.01247 / 0.60 ( 6) link_BETA1-4 : angle 2.96988 / 1.85 ( 18) link_NAG-ASN : bond 0.00507 / 0.26 ( 8) link_NAG-ASN : angle 2.01584 / 1.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.9265 (t) cc_final: 0.9030 (p) REVERT: A 408 MET cc_start: 0.8038 (mtm) cc_final: 0.7737 (mtm) REVERT: B 135 MET cc_start: 0.8328 (mmm) cc_final: 0.8011 (mmm) REVERT: E 13 LYS cc_start: 0.6585 (mmtt) cc_final: 0.6302 (mmtt) REVERT: E 43 LYS cc_start: 0.8266 (mttt) cc_final: 0.8051 (mppt) REVERT: F 35 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7931 (mtm-85) outliers start: 15 outliers final: 10 residues processed: 102 average time/residue: 0.0982 time to fit residues: 14.0350 Evaluate side-chains 86 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 54 optimal weight: 0.0470 chunk 72 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 GLN B 63 HIS E 35 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100310 restraints weight = 15104.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.103126 restraints weight = 8723.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104946 restraints weight = 6145.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106180 restraints weight = 4863.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106835 restraints weight = 4120.277| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9405 Z= 0.143 Angle : 0.572 8.294 12794 Z= 0.296 Chirality : 0.046 0.163 1454 Planarity : 0.004 0.038 1645 Dihedral : 4.529 22.767 1268 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.18 % Allowed : 8.59 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1170 helix: -0.06 (0.52), residues: 96 sheet: 0.83 (0.24), residues: 442 loop : 0.11 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 211 TYR 0.022 0.001 TYR E 100 PHE 0.012 0.001 PHE F 68 TRP 0.023 0.002 TRP A 61 HIS 0.008 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9379) covalent geometry : angle 0.55679 / 0.29 (12725) SS BOND : bond 0.00179 / 0.07 ( 9) SS BOND : angle 0.95312 / 0.46 ( 18) hydrogen bonds : bond 0.03371 / 2.14 ( 331) hydrogen bonds : angle 6.19970 / 4.25 ( 867) link_ALPHA1-2 : bond 0.00585 / 0.31 ( 1) link_ALPHA1-2 : angle 1.35810 / 1.05 ( 3) link_ALPHA1-3 : bond 0.00754 / 0.40 ( 1) link_ALPHA1-3 : angle 1.33319 / 0.93 ( 3) link_ALPHA1-6 : bond 0.00709 / 0.37 ( 1) link_ALPHA1-6 : angle 1.19339 / 1.00 ( 3) link_BETA1-4 : bond 0.01241 / 0.60 ( 6) link_BETA1-4 : angle 2.62344 / 1.64 ( 18) link_NAG-ASN : bond 0.00547 / 0.27 ( 8) link_NAG-ASN : angle 1.82013 / 1.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.9245 (t) cc_final: 0.9009 (p) REVERT: A 261 MET cc_start: 0.9157 (mmt) cc_final: 0.8928 (tpp) REVERT: A 408 MET cc_start: 0.8104 (mtm) cc_final: 0.7811 (mtm) REVERT: B 117 MET cc_start: 0.9257 (mmm) cc_final: 0.8877 (mmm) REVERT: B 278 MET cc_start: 0.8586 (mtm) cc_final: 0.8345 (mtm) REVERT: B 394 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7061 (ttp) REVERT: E 80 TYR cc_start: 0.8200 (m-80) cc_final: 0.7974 (m-80) REVERT: E 100 TYR cc_start: 0.8841 (t80) cc_final: 0.8621 (t80) outliers start: 11 outliers final: 8 residues processed: 93 average time/residue: 0.0938 time to fit residues: 12.3548 Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.0670 chunk 104 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 0.0170 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101363 restraints weight = 15236.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104278 restraints weight = 8789.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106160 restraints weight = 6165.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107216 restraints weight = 4862.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108103 restraints weight = 4187.327| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9405 Z= 0.097 Angle : 0.510 7.436 12794 Z= 0.263 Chirality : 0.044 0.158 1454 Planarity : 0.003 0.037 1645 Dihedral : 4.242 21.316 1268 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.86 % Allowed : 8.49 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1170 helix: 0.04 (0.52), residues: 102 sheet: 0.80 (0.24), residues: 438 loop : 0.02 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.012 0.001 TYR E 100 PHE 0.014 0.001 PHE A 477 TRP 0.021 0.001 TRP A 61 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 9379) covalent geometry : angle 0.49856 / 0.26 (12725) SS BOND : bond 0.00135 / 0.06 ( 9) SS BOND : angle 0.61466 / 0.33 ( 18) hydrogen bonds : bond 0.02803 / 1.77 ( 331) hydrogen bonds : angle 5.75336 / 3.95 ( 867) link_ALPHA1-2 : bond 0.00433 / 0.23 ( 1) link_ALPHA1-2 : angle 1.40899 / 1.15 ( 3) link_ALPHA1-3 : bond 0.00579 / 0.30 ( 1) link_ALPHA1-3 : angle 1.27001 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00684 / 0.36 ( 1) link_ALPHA1-6 : angle 1.23388 / 1.03 ( 3) link_BETA1-4 : bond 0.01119 / 0.55 ( 6) link_BETA1-4 : angle 2.30029 / 1.47 ( 18) link_NAG-ASN : bond 0.00444 / 0.22 ( 8) link_NAG-ASN : angle 1.47750 / 0.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.9198 (t) cc_final: 0.8979 (p) REVERT: A 408 MET cc_start: 0.8046 (mtm) cc_final: 0.7776 (mtm) REVERT: B 278 MET cc_start: 0.8492 (mtm) cc_final: 0.8221 (mtm) REVERT: B 394 MET cc_start: 0.7374 (ttm) cc_final: 0.7035 (ttp) REVERT: E 80 TYR cc_start: 0.7970 (m-80) cc_final: 0.7739 (m-10) REVERT: F 34 THR cc_start: 0.9096 (p) cc_final: 0.8810 (m) REVERT: F 35 ARG cc_start: 0.8359 (mpp80) cc_final: 0.7803 (mtm-85) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.0942 time to fit residues: 11.9001 Evaluate side-chains 83 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 87 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN E 3 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098377 restraints weight = 15236.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101211 restraints weight = 8833.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103038 restraints weight = 6228.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104233 restraints weight = 4929.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104984 restraints weight = 4195.142| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9405 Z= 0.148 Angle : 0.532 7.815 12794 Z= 0.272 Chirality : 0.045 0.161 1454 Planarity : 0.003 0.036 1645 Dihedral : 4.209 20.099 1268 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.07 % Allowed : 8.81 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1170 helix: 0.07 (0.53), residues: 97 sheet: 0.67 (0.23), residues: 445 loop : -0.01 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 211 TYR 0.013 0.001 TYR F 55 PHE 0.015 0.001 PHE A 427 TRP 0.015 0.001 TRP A 61 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9379) covalent geometry : angle 0.51922 / 0.27 (12725) SS BOND : bond 0.00197 / 0.08 ( 9) SS BOND : angle 0.87366 / 0.48 ( 18) hydrogen bonds : bond 0.02893 / 1.84 ( 331) hydrogen bonds : angle 5.65363 / 3.87 ( 867) link_ALPHA1-2 : bond 0.00454 / 0.24 ( 1) link_ALPHA1-2 : angle 1.32158 / 1.08 ( 3) link_ALPHA1-3 : bond 0.00564 / 0.30 ( 1) link_ALPHA1-3 : angle 1.30609 / 0.97 ( 3) link_ALPHA1-6 : bond 0.00587 / 0.31 ( 1) link_ALPHA1-6 : angle 1.25986 / 1.10 ( 3) link_BETA1-4 : bond 0.01015 / 0.49 ( 6) link_BETA1-4 : angle 2.45049 / 1.58 ( 18) link_NAG-ASN : bond 0.00333 / 0.17 ( 8) link_NAG-ASN : angle 1.53061 / 0.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8160 (mtm) cc_final: 0.7925 (mtm) REVERT: B 278 MET cc_start: 0.8530 (mtm) cc_final: 0.8250 (mtm) REVERT: B 394 MET cc_start: 0.7362 (ttm) cc_final: 0.7041 (ttp) REVERT: E 80 TYR cc_start: 0.8049 (m-80) cc_final: 0.7818 (m-10) REVERT: F 35 ARG cc_start: 0.8350 (mpp80) cc_final: 0.7971 (mtm-85) REVERT: F 42 TYR cc_start: 0.9316 (m-80) cc_final: 0.8702 (m-10) outliers start: 10 outliers final: 9 residues processed: 88 average time/residue: 0.0955 time to fit residues: 11.9453 Evaluate side-chains 84 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 280 HIS ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095384 restraints weight = 15152.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098119 restraints weight = 8909.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099870 restraints weight = 6370.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100943 restraints weight = 5100.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101760 restraints weight = 4411.451| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9405 Z= 0.211 Angle : 0.594 8.164 12794 Z= 0.302 Chirality : 0.047 0.172 1454 Planarity : 0.004 0.041 1645 Dihedral : 4.446 18.456 1268 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.40 % Allowed : 9.02 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1170 helix: -0.25 (0.53), residues: 97 sheet: 0.40 (0.23), residues: 447 loop : -0.20 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.018 0.001 TYR A 254 PHE 0.021 0.002 PHE A 427 TRP 0.014 0.002 TRP B 230 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 ( 9379) covalent geometry : angle 0.58056 / 0.30 (12725) SS BOND : bond 0.00244 / 0.10 ( 9) SS BOND : angle 1.02547 / 0.53 ( 18) hydrogen bonds : bond 0.03225 / 2.04 ( 331) hydrogen bonds : angle 5.73466 / 3.93 ( 867) link_ALPHA1-2 : bond 0.00476 / 0.25 ( 1) link_ALPHA1-2 : angle 1.28113 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00683 / 0.36 ( 1) link_ALPHA1-3 : angle 1.33154 / 0.94 ( 3) link_ALPHA1-6 : bond 0.00431 / 0.23 ( 1) link_ALPHA1-6 : angle 1.28777 / 1.16 ( 3) link_BETA1-4 : bond 0.00958 / 0.46 ( 6) link_BETA1-4 : angle 2.61304 / 1.71 ( 18) link_NAG-ASN : bond 0.00274 / 0.14 ( 8) link_NAG-ASN : angle 1.72608 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 278 MET cc_start: 0.8603 (mtm) cc_final: 0.8359 (mtm) REVERT: B 394 MET cc_start: 0.7432 (ttm) cc_final: 0.7129 (ttp) REVERT: E 11 LEU cc_start: 0.7283 (tt) cc_final: 0.6789 (mp) REVERT: E 80 TYR cc_start: 0.8189 (m-80) cc_final: 0.7912 (m-10) REVERT: E 104 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7900 (p0) REVERT: F 35 ARG cc_start: 0.8401 (mpp80) cc_final: 0.7935 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.0969 time to fit residues: 11.7569 Evaluate side-chains 81 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097756 restraints weight = 15129.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100607 restraints weight = 8820.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102435 restraints weight = 6227.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103476 restraints weight = 4949.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104311 restraints weight = 4274.379| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9405 Z= 0.111 Angle : 0.521 7.508 12794 Z= 0.266 Chirality : 0.045 0.166 1454 Planarity : 0.003 0.038 1645 Dihedral : 4.250 18.874 1268 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.86 % Allowed : 10.10 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1170 helix: -0.12 (0.53), residues: 97 sheet: 0.48 (0.23), residues: 447 loop : -0.07 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.010 0.001 TYR B 109 PHE 0.008 0.001 PHE A 231 TRP 0.013 0.001 TRP A 61 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9379) covalent geometry : angle 0.50926 / 0.26 (12725) SS BOND : bond 0.00274 / 0.11 ( 9) SS BOND : angle 0.91713 / 0.51 ( 18) hydrogen bonds : bond 0.02707 / 1.69 ( 331) hydrogen bonds : angle 5.50950 / 3.77 ( 867) link_ALPHA1-2 : bond 0.00470 / 0.25 ( 1) link_ALPHA1-2 : angle 1.31737 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00517 / 0.27 ( 1) link_ALPHA1-3 : angle 1.24700 / 0.97 ( 3) link_ALPHA1-6 : bond 0.00628 / 0.33 ( 1) link_ALPHA1-6 : angle 1.20933 / 1.03 ( 3) link_BETA1-4 : bond 0.01112 / 0.54 ( 6) link_BETA1-4 : angle 2.22770 / 1.44 ( 18) link_NAG-ASN : bond 0.00307 / 0.16 ( 8) link_NAG-ASN : angle 1.44000 / 0.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.8109 (t0) cc_final: 0.7806 (m-30) REVERT: B 278 MET cc_start: 0.8481 (mtm) cc_final: 0.8212 (mtm) REVERT: B 394 MET cc_start: 0.7414 (ttm) cc_final: 0.7128 (ttp) REVERT: E 11 LEU cc_start: 0.7265 (tt) cc_final: 0.6806 (mp) REVERT: E 80 TYR cc_start: 0.8196 (m-80) cc_final: 0.7952 (m-10) REVERT: F 35 ARG cc_start: 0.8440 (mpp80) cc_final: 0.7961 (mtm-85) REVERT: F 42 TYR cc_start: 0.9366 (m-80) cc_final: 0.8783 (m-10) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.0930 time to fit residues: 11.0712 Evaluate side-chains 82 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.0980 chunk 106 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099594 restraints weight = 14892.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.102398 restraints weight = 8616.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104203 restraints weight = 6090.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105412 restraints weight = 4829.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106091 restraints weight = 4105.500| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9405 Z= 0.092 Angle : 0.503 10.784 12794 Z= 0.255 Chirality : 0.044 0.165 1454 Planarity : 0.003 0.041 1645 Dihedral : 4.096 18.106 1268 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.86 % Allowed : 10.10 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1170 helix: 0.06 (0.53), residues: 97 sheet: 0.51 (0.24), residues: 447 loop : -0.06 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.010 0.001 TYR E 100 PHE 0.008 0.001 PHE B 93 TRP 0.026 0.001 TRP A 61 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 9379) covalent geometry : angle 0.49200 / 0.25 (12725) SS BOND : bond 0.00122 / 0.06 ( 9) SS BOND : angle 0.97122 / 0.58 ( 18) hydrogen bonds : bond 0.02529 / 1.57 ( 331) hydrogen bonds : angle 5.34528 / 3.65 ( 867) link_ALPHA1-2 : bond 0.00437 / 0.23 ( 1) link_ALPHA1-2 : angle 1.36723 / 1.12 ( 3) link_ALPHA1-3 : bond 0.00544 / 0.29 ( 1) link_ALPHA1-3 : angle 1.30014 / 1.03 ( 3) link_ALPHA1-6 : bond 0.00622 / 0.33 ( 1) link_ALPHA1-6 : angle 1.23628 / 1.06 ( 3) link_BETA1-4 : bond 0.01040 / 0.51 ( 6) link_BETA1-4 : angle 2.07997 / 1.34 ( 18) link_NAG-ASN : bond 0.00267 / 0.14 ( 8) link_NAG-ASN : angle 1.40764 / 0.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.8091 (t0) cc_final: 0.7734 (m-30) REVERT: B 172 TYR cc_start: 0.8015 (m-80) cc_final: 0.7715 (m-10) REVERT: B 394 MET cc_start: 0.7393 (ttm) cc_final: 0.7112 (ttp) REVERT: E 80 TYR cc_start: 0.8145 (m-80) cc_final: 0.7841 (m-10) REVERT: F 4 MET cc_start: 0.8549 (mmm) cc_final: 0.8307 (tpt) REVERT: F 35 ARG cc_start: 0.8277 (mpp80) cc_final: 0.7846 (mtm-85) REVERT: F 42 TYR cc_start: 0.9353 (m-80) cc_final: 0.8797 (m-10) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.0899 time to fit residues: 11.2295 Evaluate side-chains 83 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 100 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098528 restraints weight = 15042.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101315 restraints weight = 8775.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103094 restraints weight = 6198.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104248 restraints weight = 4925.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.104915 restraints weight = 4217.439| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9405 Z= 0.118 Angle : 0.516 9.002 12794 Z= 0.263 Chirality : 0.044 0.164 1454 Planarity : 0.003 0.041 1645 Dihedral : 4.069 17.237 1268 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.97 % Allowed : 10.31 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1170 helix: 0.05 (0.53), residues: 97 sheet: 0.50 (0.24), residues: 447 loop : -0.07 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.010 0.001 TYR F 55 PHE 0.012 0.001 PHE A 427 TRP 0.027 0.001 TRP A 61 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9379) covalent geometry : angle 0.50363 / 0.26 (12725) SS BOND : bond 0.00233 / 0.09 ( 9) SS BOND : angle 1.08876 / 0.65 ( 18) hydrogen bonds : bond 0.02618 / 1.63 ( 331) hydrogen bonds : angle 5.33311 / 3.65 ( 867) link_ALPHA1-2 : bond 0.00453 / 0.24 ( 1) link_ALPHA1-2 : angle 1.33952 / 1.10 ( 3) link_ALPHA1-3 : bond 0.00556 / 0.29 ( 1) link_ALPHA1-3 : angle 1.29548 / 1.00 ( 3) link_ALPHA1-6 : bond 0.00574 / 0.30 ( 1) link_ALPHA1-6 : angle 1.25623 / 1.09 ( 3) link_BETA1-4 : bond 0.01003 / 0.49 ( 6) link_BETA1-4 : angle 2.15770 / 1.41 ( 18) link_NAG-ASN : bond 0.00226 / 0.12 ( 8) link_NAG-ASN : angle 1.49180 / 0.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.8103 (t0) cc_final: 0.7744 (m-30) REVERT: B 172 TYR cc_start: 0.8033 (m-80) cc_final: 0.7743 (m-10) REVERT: B 394 MET cc_start: 0.7410 (ttm) cc_final: 0.7139 (ttp) REVERT: E 80 TYR cc_start: 0.8163 (m-80) cc_final: 0.7872 (m-10) REVERT: F 35 ARG cc_start: 0.8307 (mpp80) cc_final: 0.7832 (mtm-85) REVERT: F 42 TYR cc_start: 0.9357 (m-80) cc_final: 0.8808 (m-10) outliers start: 9 outliers final: 9 residues processed: 85 average time/residue: 0.0956 time to fit residues: 11.4695 Evaluate side-chains 85 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.0970 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097343 restraints weight = 15079.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100079 restraints weight = 8877.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.101907 restraints weight = 6329.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102895 restraints weight = 5031.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103773 restraints weight = 4365.380| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9405 Z= 0.145 Angle : 0.527 7.279 12794 Z= 0.270 Chirality : 0.045 0.163 1454 Planarity : 0.004 0.045 1645 Dihedral : 4.098 16.910 1268 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.97 % Allowed : 10.74 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1170 helix: -0.00 (0.53), residues: 97 sheet: 0.44 (0.24), residues: 447 loop : -0.09 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.012 0.001 TYR A 254 PHE 0.014 0.001 PHE A 427 TRP 0.035 0.002 TRP A 61 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9379) covalent geometry : angle 0.51523 / 0.27 (12725) SS BOND : bond 0.00178 / 0.07 ( 9) SS BOND : angle 0.74984 / 0.38 ( 18) hydrogen bonds : bond 0.02696 / 1.69 ( 331) hydrogen bonds : angle 5.33385 / 3.65 ( 867) link_ALPHA1-2 : bond 0.00465 / 0.24 ( 1) link_ALPHA1-2 : angle 1.30536 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00560 / 0.29 ( 1) link_ALPHA1-3 : angle 1.29173 / 0.99 ( 3) link_ALPHA1-6 : bond 0.00535 / 0.28 ( 1) link_ALPHA1-6 : angle 1.27490 / 1.12 ( 3) link_BETA1-4 : bond 0.00966 / 0.47 ( 6) link_BETA1-4 : angle 2.20456 / 1.45 ( 18) link_NAG-ASN : bond 0.00212 / 0.12 ( 8) link_NAG-ASN : angle 1.53259 / 0.96 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: B 172 TYR cc_start: 0.8060 (m-80) cc_final: 0.7764 (m-10) REVERT: B 394 MET cc_start: 0.7446 (ttm) cc_final: 0.7187 (ttp) REVERT: E 80 TYR cc_start: 0.8196 (m-80) cc_final: 0.7912 (m-10) REVERT: F 4 MET cc_start: 0.8733 (tpt) cc_final: 0.8130 (tpt) REVERT: F 35 ARG cc_start: 0.8303 (mpp80) cc_final: 0.7769 (mtm-85) REVERT: F 42 TYR cc_start: 0.9360 (m-80) cc_final: 0.8822 (m-10) outliers start: 9 outliers final: 9 residues processed: 88 average time/residue: 0.0981 time to fit residues: 12.2249 Evaluate side-chains 84 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 GLU Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.084203 restraints weight = 15880.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.086122 restraints weight = 10835.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.087413 restraints weight = 8432.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.088286 restraints weight = 7105.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088825 restraints weight = 6311.510| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9405 Z= 0.191 Angle : 0.575 7.385 12794 Z= 0.295 Chirality : 0.046 0.164 1454 Planarity : 0.004 0.043 1645 Dihedral : 4.286 18.290 1268 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.18 % Allowed : 10.85 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1170 helix: -0.18 (0.53), residues: 97 sheet: 0.34 (0.24), residues: 445 loop : -0.20 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 33 TYR 0.016 0.001 TYR A 254 PHE 0.020 0.002 PHE A 427 TRP 0.038 0.002 TRP A 61 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 9379) covalent geometry : angle 0.56299 / 0.29 (12725) SS BOND : bond 0.00221 / 0.09 ( 9) SS BOND : angle 0.93514 / 0.47 ( 18) hydrogen bonds : bond 0.03060 / 1.90 ( 331) hydrogen bonds : angle 5.46344 / 3.75 ( 867) link_ALPHA1-2 : bond 0.00470 / 0.25 ( 1) link_ALPHA1-2 : angle 1.25908 / 1.04 ( 3) link_ALPHA1-3 : bond 0.00562 / 0.30 ( 1) link_ALPHA1-3 : angle 1.28103 / 0.95 ( 3) link_ALPHA1-6 : bond 0.00470 / 0.25 ( 1) link_ALPHA1-6 : angle 1.33030 / 1.20 ( 3) link_BETA1-4 : bond 0.00978 / 0.47 ( 6) link_BETA1-4 : angle 2.22977 / 1.47 ( 18) link_NAG-ASN : bond 0.00348 / 0.18 ( 8) link_NAG-ASN : angle 1.77174 / 1.11 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.21 seconds wall clock time: 26 minutes 45.70 seconds (1605.70 seconds total)