Starting phenix.real_space_refine on Fri Mar 14 00:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ujb_20795/03_2025/6ujb_20795.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujb_20795/03_2025/6ujb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2025/6ujb_20795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2025/6ujb_20795.map" model { file = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2025/6ujb_20795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujb_20795/03_2025/6ujb_20795.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.15, per 1000 atoms: 0.67 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: 2.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.35 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: 3.19 Time building geometry restraints manager: 3.28 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 - 21.42: 5640 21.42 - 42.83: 122 42.83 - 64.25: 37 64.25 - 85.67: 17 85.67 - 107.08: 7 Dihedral angle restraints: 5823 sinusoidal: 2433 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 5820 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.014 0.086 9379 Z= 0.952 Angle : 1.445 38.841 12725 Z= 0.955 Chirality : 0.084 0.354 1454 Planarity : 0.006 0.027 1645 Dihedral : 11.747 107.084 3628 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (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 TRP 0.023 0.006 TRP A 179 HIS 0.003 0.001 HIS B 227 PHE 0.021 0.004 PHE A 276 TYR 0.034 0.005 TYR A 254 ARG 0.005 0.001 ARG B 231 *********************** 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 : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7791 (t0) cc_final: 0.7580 (t0) 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: 0.7786 (mmm) REVERT: E 43 LYS cc_start: 0.8264 (mttt) cc_final: 0.7990 (mppt) REVERT: E 50 ARG cc_start: 0.7997 (ptm-80) cc_final: 0.7745 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2920 time to fit residues: 67.2846 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 : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3668 r_free = 0.3668 target = 0.123556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102821 restraints weight = 15264.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105604 restraints weight = 9105.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107400 restraints weight = 6514.734| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9379 Z= 0.290 Angle : 0.641 8.429 12725 Z= 0.340 Chirality : 0.048 0.254 1454 Planarity : 0.004 0.037 1645 Dihedral : 7.827 88.621 1617 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.72 % Allowed : 6.66 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1170 helix: -0.36 (0.51), residues: 96 sheet: 0.65 (0.23), residues: 463 loop : 0.25 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 61 HIS 0.004 0.001 HIS B 161 PHE 0.016 0.002 PHE F 68 TYR 0.014 0.002 TYR A 112 ARG 0.005 0.001 ARG B 133 *********************** 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 109 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.9265 (t) cc_final: 0.9037 (p) REVERT: A 408 MET cc_start: 0.8043 (mtm) cc_final: 0.7747 (mtm) REVERT: B 135 MET cc_start: 0.8328 (mmm) cc_final: 0.7997 (mmm) REVERT: E 13 LYS cc_start: 0.6589 (mmtt) cc_final: 0.6314 (mmtt) REVERT: E 43 LYS cc_start: 0.8284 (mttt) cc_final: 0.8071 (mppt) REVERT: F 35 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7983 (mtm-85) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.2323 time to fit residues: 32.7001 Evaluate side-chains 87 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 79 optimal weight: 0.0000 chunk 112 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 85 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3645 r_free = 0.3645 target = 0.121385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100962 restraints weight = 15095.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103884 restraints weight = 8601.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105741 restraints weight = 6009.278| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9379 Z= 0.180 Angle : 0.548 7.024 12725 Z= 0.287 Chirality : 0.046 0.283 1454 Planarity : 0.004 0.039 1645 Dihedral : 6.887 77.921 1617 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.07 % Allowed : 8.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1170 helix: 0.03 (0.53), residues: 96 sheet: 0.82 (0.24), residues: 435 loop : 0.12 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 61 HIS 0.008 0.001 HIS B 63 PHE 0.011 0.001 PHE B 306 TYR 0.023 0.001 TYR E 100 ARG 0.006 0.000 ARG A 211 *********************** 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 100 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 SER cc_start: 0.9267 (t) cc_final: 0.9018 (p) REVERT: A 408 MET cc_start: 0.8087 (mtm) cc_final: 0.7803 (mtm) REVERT: B 117 MET cc_start: 0.9256 (mmm) cc_final: 0.8855 (mmm) REVERT: B 135 MET cc_start: 0.8117 (mmm) cc_final: 0.7808 (mmm) REVERT: B 394 MET cc_start: 0.7367 (ttm) cc_final: 0.6980 (ttp) REVERT: E 100 TYR cc_start: 0.8826 (t80) cc_final: 0.8606 (t80) REVERT: F 34 THR cc_start: 0.9132 (p) cc_final: 0.8838 (m) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.2213 time to fit residues: 29.5384 Evaluate side-chains 85 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 2 optimal weight: 0.0370 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.121765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101177 restraints weight = 15025.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103973 restraints weight = 8904.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105775 restraints weight = 6324.319| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9379 Z= 0.185 Angle : 0.518 6.591 12725 Z= 0.268 Chirality : 0.045 0.296 1454 Planarity : 0.004 0.038 1645 Dihedral : 6.398 70.942 1617 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.18 % Allowed : 8.38 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1170 helix: 0.05 (0.53), residues: 101 sheet: 0.76 (0.24), residues: 437 loop : 0.00 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 61 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 477 TYR 0.011 0.001 TYR E 100 ARG 0.003 0.000 ARG A 211 *********************** 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 93 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8097 (mtm) cc_final: 0.7830 (mtm) REVERT: B 394 MET cc_start: 0.7428 (ttm) cc_final: 0.7074 (ttp) REVERT: E 13 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6914 (mmtt) REVERT: E 87 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7316 (pttm) REVERT: E 100 TYR cc_start: 0.8622 (t80) cc_final: 0.8334 (t80) REVERT: F 35 ARG cc_start: 0.8361 (mpp80) cc_final: 0.7835 (mtm-85) REVERT: F 110 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6874 (mt-10) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.2508 time to fit residues: 30.5010 Evaluate side-chains 88 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 69 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 68 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 0.0570 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3628 r_free = 0.3628 target = 0.120288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099957 restraints weight = 14846.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102790 restraints weight = 8621.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104581 restraints weight = 6067.358| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9379 Z= 0.168 Angle : 0.496 7.368 12725 Z= 0.258 Chirality : 0.045 0.300 1454 Planarity : 0.003 0.037 1645 Dihedral : 5.953 63.931 1617 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.29 % Allowed : 8.16 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1170 helix: 0.18 (0.54), residues: 97 sheet: 0.71 (0.24), residues: 443 loop : 0.04 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 61 HIS 0.002 0.001 HIS B 166 PHE 0.010 0.001 PHE A 427 TYR 0.010 0.001 TYR E 80 ARG 0.003 0.000 ARG A 211 *********************** 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 99 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.8078 (t0) cc_final: 0.7763 (m-30) REVERT: A 408 MET cc_start: 0.8027 (mtm) cc_final: 0.7811 (mtm) REVERT: B 394 MET cc_start: 0.7413 (ttm) cc_final: 0.7098 (ttp) REVERT: E 87 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7322 (pttm) REVERT: F 35 ARG cc_start: 0.8372 (mpp80) cc_final: 0.7872 (mtm-85) REVERT: F 42 TYR cc_start: 0.9291 (m-80) cc_final: 0.8693 (m-10) outliers start: 12 outliers final: 11 residues processed: 93 average time/residue: 0.2511 time to fit residues: 32.3272 Evaluate side-chains 86 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 64 VAL 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 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 58 optimal weight: 0.0670 chunk 45 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3604 r_free = 0.3604 target = 0.118950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098105 restraints weight = 15125.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100912 restraints weight = 8849.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102732 restraints weight = 6283.920| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9379 Z= 0.220 Angle : 0.528 7.450 12725 Z= 0.271 Chirality : 0.046 0.304 1454 Planarity : 0.003 0.034 1645 Dihedral : 5.835 60.409 1617 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.29 % Allowed : 8.70 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1170 helix: 0.09 (0.54), residues: 97 sheet: 0.61 (0.23), residues: 448 loop : -0.00 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 61 HIS 0.002 0.001 HIS B 161 PHE 0.014 0.001 PHE A 427 TYR 0.011 0.001 TYR F 55 ARG 0.002 0.000 ARG A 211 *********************** 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 93 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 302 ASP cc_start: 0.8125 (t0) cc_final: 0.7766 (m-30) REVERT: A 408 MET cc_start: 0.8131 (mtm) cc_final: 0.7897 (mtm) REVERT: B 394 MET cc_start: 0.7519 (ttm) cc_final: 0.7177 (ttp) REVERT: E 11 LEU cc_start: 0.7342 (tt) cc_final: 0.6897 (mp) REVERT: E 13 LYS cc_start: 0.6508 (mmtt) cc_final: 0.6189 (mmtt) REVERT: E 87 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7432 (pttm) REVERT: F 35 ARG cc_start: 0.8450 (mpp80) cc_final: 0.7914 (mtm-85) REVERT: F 42 TYR cc_start: 0.9348 (m-80) cc_final: 0.8766 (m-10) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.2446 time to fit residues: 30.1725 Evaluate side-chains 81 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE 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 86 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3600 r_free = 0.3600 target = 0.118690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097753 restraints weight = 15300.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100554 restraints weight = 8951.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102359 restraints weight = 6390.430| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9379 Z= 0.209 Angle : 0.512 7.123 12725 Z= 0.264 Chirality : 0.045 0.296 1454 Planarity : 0.004 0.050 1645 Dihedral : 5.665 56.220 1617 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.18 % Allowed : 8.81 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1170 helix: 0.06 (0.53), residues: 97 sheet: 0.57 (0.23), residues: 450 loop : -0.03 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 61 HIS 0.002 0.001 HIS E 35 PHE 0.012 0.001 PHE A 427 TYR 0.011 0.001 TYR A 254 ARG 0.002 0.000 ARG A 211 *********************** 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 93 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7292 (tt0) cc_final: 0.6976 (tt0) REVERT: A 302 ASP cc_start: 0.8112 (t0) cc_final: 0.7819 (m-30) REVERT: A 408 MET cc_start: 0.8066 (mtm) cc_final: 0.7857 (mtm) REVERT: B 394 MET cc_start: 0.7508 (ttm) cc_final: 0.7241 (ttp) REVERT: B 415 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8439 (mt-10) REVERT: E 87 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7199 (pttm) REVERT: F 34 THR cc_start: 0.9071 (p) cc_final: 0.8796 (m) REVERT: F 35 ARG cc_start: 0.8425 (mpp80) cc_final: 0.7836 (mtm-85) REVERT: F 42 TYR cc_start: 0.9365 (m-80) cc_final: 0.8797 (m-10) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.2250 time to fit residues: 27.7927 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 : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3568 r_free = 0.3568 target = 0.116457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.095390 restraints weight = 15482.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098130 restraints weight = 9117.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099924 restraints weight = 6538.446| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9379 Z= 0.290 Angle : 0.549 6.777 12725 Z= 0.284 Chirality : 0.047 0.301 1454 Planarity : 0.004 0.040 1645 Dihedral : 5.662 52.643 1617 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.18 % Allowed : 9.45 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1170 helix: -0.10 (0.53), residues: 97 sheet: 0.48 (0.23), residues: 446 loop : -0.16 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 61 HIS 0.010 0.001 HIS B 63 PHE 0.020 0.002 PHE A 427 TYR 0.017 0.001 TYR A 254 ARG 0.002 0.000 ARG A 211 *********************** 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: 11 poor density : 79 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: B 241 MET cc_start: 0.8480 (ttm) cc_final: 0.8216 (ttm) REVERT: B 394 MET cc_start: 0.7549 (ttm) cc_final: 0.7283 (ttp) REVERT: E 87 LYS cc_start: 0.7567 (mtmm) cc_final: 0.7235 (pttm) REVERT: F 35 ARG cc_start: 0.8338 (mpp80) cc_final: 0.7880 (mtm-85) REVERT: F 42 TYR cc_start: 0.9351 (m-80) cc_final: 0.8837 (m-10) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.2383 time to fit residues: 28.9323 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 : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3586 r_free = 0.3586 target = 0.117772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096941 restraints weight = 15108.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099696 restraints weight = 8959.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101488 restraints weight = 6410.391| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9379 Z= 0.194 Angle : 0.514 6.595 12725 Z= 0.266 Chirality : 0.046 0.283 1454 Planarity : 0.003 0.040 1645 Dihedral : 5.520 50.484 1617 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.07 % Allowed : 9.77 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1170 helix: -0.00 (0.53), residues: 97 sheet: 0.56 (0.23), residues: 446 loop : -0.20 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 61 HIS 0.004 0.001 HIS B 63 PHE 0.012 0.001 PHE A 427 TYR 0.011 0.001 TYR A 254 ARG 0.002 0.000 ARG A 211 *********************** 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 94 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: B 394 MET cc_start: 0.7539 (ttm) cc_final: 0.7265 (ttp) REVERT: E 87 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7334 (pttm) REVERT: F 34 THR cc_start: 0.8965 (p) cc_final: 0.8721 (m) REVERT: F 35 ARG cc_start: 0.8297 (mpp80) cc_final: 0.7720 (mtm-85) REVERT: F 42 TYR cc_start: 0.9291 (m-80) cc_final: 0.8711 (m-10) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.2711 time to fit residues: 35.5202 Evaluate side-chains 86 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE 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 87 optimal weight: 0.0370 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3587 r_free = 0.3587 target = 0.117721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096877 restraints weight = 15421.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099652 restraints weight = 9023.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101493 restraints weight = 6421.349| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9379 Z= 0.196 Angle : 0.520 6.181 12725 Z= 0.270 Chirality : 0.046 0.275 1454 Planarity : 0.004 0.043 1645 Dihedral : 5.410 48.454 1617 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.18 % Allowed : 9.99 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1170 helix: 0.01 (0.53), residues: 97 sheet: 0.51 (0.23), residues: 451 loop : -0.19 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 61 HIS 0.004 0.001 HIS B 63 PHE 0.012 0.001 PHE A 427 TYR 0.011 0.001 TYR A 254 ARG 0.002 0.000 ARG A 211 ********************** 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 89 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.391 Fit side-chains REVERT: A 302 ASP cc_start: 0.8012 (t0) cc_final: 0.7795 (m-30) REVERT: B 394 MET cc_start: 0.7523 (ttm) cc_final: 0.7265 (ttp) REVERT: E 87 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7305 (pttm) REVERT: F 34 THR cc_start: 0.8941 (p) cc_final: 0.8688 (m) REVERT: F 35 ARG cc_start: 0.8301 (mpp80) cc_final: 0.7725 (mtm-85) REVERT: F 42 TYR cc_start: 0.9315 (m-80) cc_final: 0.8747 (m-10) outliers start: 11 outliers final: 11 residues processed: 85 average time/residue: 0.3246 time to fit residues: 39.1278 Evaluate side-chains 82 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ILE 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 60 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 75 optimal weight: 0.0040 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3355 r_free = 0.3355 target = 0.105863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.086536 restraints weight = 15882.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.088536 restraints weight = 10669.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.089813 restraints weight = 8192.815| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9379 Z= 0.212 Angle : 0.530 7.460 12725 Z= 0.275 Chirality : 0.046 0.269 1454 Planarity : 0.004 0.044 1645 Dihedral : 5.318 46.243 1617 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.29 % Allowed : 10.31 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1170 helix: -0.02 (0.53), residues: 97 sheet: 0.47 (0.23), residues: 451 loop : -0.20 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 61 HIS 0.004 0.001 HIS B 63 PHE 0.013 0.001 PHE A 427 TYR 0.012 0.001 TYR A 254 ARG 0.005 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.37 seconds wall clock time: 53 minutes 32.42 seconds (3212.42 seconds total)