Starting phenix.real_space_refine on Fri Sep 11 12:49:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.map" model { file = "/net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ujc_20796/09_2026/6ujc_20796.cif" } resolution = 3.56 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= 0.002 sd= 0.048 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 5803 2.51 5 N 1553 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 9209 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: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2811 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 4} 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: 11 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: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 112} 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: 2.08, per 1000 atoms: 0.23 Number of scatterers: 9209 At special positions: 0 Unit cell: (72.63, 100.875, 164.09, 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 1804 8.00 N 1553 7.00 C 5803 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=2.02 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.16 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 265 " distance=2.02 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 377 " distance=2.04 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 98 " distance=2.04 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: 0.97 Conformation dependent library (CDL) restraints added in 374.3 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 13.3% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 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 126 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.810A pdb=" N HIS B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (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: 4.032A 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 31 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 'F' and resid 89 through 93 removed outlier: 3.852A pdb=" N LEU F 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 12 removed outlier: 4.034A pdb=" N ARG A 436 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASP A 6 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N LEU A 434 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N ALA A 432 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP A 421 " --> pdb=" O ALA A 411 " (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: 7.010A 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 98 through 101 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.537A pdb=" N SER A 160 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.513A 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: 6.498A pdb=" N VAL A 253 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 266 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.572A 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: 5.665A pdb=" N ASP A 357 " --> pdb=" O LEU A 347 " (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 511 through 513 Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.746A pdb=" N LEU A 454 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.554A pdb=" N CYS A 461 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.654A pdb=" N VAL B 81 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N HIS B 422 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.326A 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: 5.330A pdb=" N HIS B 184 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 148 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 188 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 144 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR B 103 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 141 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ILE B 320 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 297 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY B 322 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 6.202A 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: 6.453A pdb=" N MET E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.760A 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 4 through 7 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.808A pdb=" N LEU F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR F 59 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP F 45 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 344 hydrogen bonds defined for protein. 873 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: 1.84 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: 1936 1.32 - 1.45: 2441 1.45 - 1.58: 4947 1.58 - 1.71: 5 1.71 - 1.84: 66 Bond restraints: 9395 Sorted by residual: bond pdb=" NE ARG F 32 " pdb=" CZ ARG F 32 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.21e+01 bond pdb=" CG PHE A 1 " pdb=" CD1 PHE A 1 " ideal model delta sigma weight residual 1.384 1.456 -0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+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 1.13e+01 ... (remaining 9390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 10563 1.71 - 3.42: 1768 3.42 - 5.13: 314 5.13 - 6.84: 85 6.84 - 8.54: 14 Bond angle restraints: 12744 Sorted by residual: angle pdb=" C ALA A 362 " pdb=" N PRO A 363 " pdb=" CA PRO A 363 " ideal model delta sigma weight residual 119.56 128.10 -8.54 1.02e+00 9.61e-01 7.02e+01 angle pdb=" C ALA A 40 " pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 119.56 128.02 -8.46 1.02e+00 9.61e-01 6.88e+01 angle pdb=" C ALA A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.27e+01 angle pdb=" C ALA A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta sigma weight residual 119.56 127.45 -7.89 1.02e+00 9.61e-01 5.98e+01 angle pdb=" C LEU A 463 " pdb=" N PRO A 464 " pdb=" CA PRO A 464 " ideal model delta sigma weight residual 119.78 127.54 -7.76 1.03e+00 9.43e-01 5.68e+01 ... (remaining 12739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5298 17.71 - 35.42: 121 35.42 - 53.13: 31 53.13 - 70.84: 22 70.84 - 88.55: 11 Dihedral angle restraints: 5483 sinusoidal: 2088 harmonic: 3395 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 41.37 51.63 1 1.00e+01 1.00e-02 3.64e+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 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.19 34.81 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 5480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 998 0.074 - 0.148: 342 0.148 - 0.221: 74 0.221 - 0.295: 27 0.295 - 0.369: 15 Chirality restraints: 1456 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 2.28 0.12 2.00e-02 2.50e+03 3.90e+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 -2.28 -0.12 2.00e-02 2.50e+03 3.50e+01 chirality pdb=" C1 MAN C 6 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 6 " pdb=" O5 MAN C 6 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.33e+01 ... (remaining 1453 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 260 " 0.030 2.00e-02 2.50e+03 3.09e-02 1.19e+01 pdb=" CG ASN A 260 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 260 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 260 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG A2005 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 44 " -0.027 2.00e-02 2.50e+03 2.82e-02 9.93e+00 pdb=" CG ASN A 44 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 44 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 44 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 103 " 0.030 2.00e-02 2.50e+03 1.54e-02 4.75e+00 pdb=" CG TYR B 103 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 103 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 103 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 103 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 103 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 103 " 0.018 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 30 2.41 - 3.04: 5613 3.04 - 3.66: 12870 3.66 - 4.28: 21662 4.28 - 4.90: 34679 Nonbonded interactions: 74854 Sorted by model distance: nonbonded pdb=" OE2 GLU B 212 " pdb="MG MG B2002 " model vdw 1.792 2.170 nonbonded pdb=" OD1 ASP F 34 " pdb="MG MG B2002 " model vdw 1.885 2.170 nonbonded pdb=" OD2 ASP F 34 " pdb="MG MG B2002 " model vdw 1.901 2.170 nonbonded pdb=" OG SER B 114 " pdb="MG MG B2002 " model vdw 2.003 2.170 nonbonded pdb=" OD1 ASP A 415 " pdb="CA CA A2003 " model vdw 2.081 2.510 ... (remaining 74849 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 0.129 9421 Z= 0.760 Angle : 1.406 8.544 12813 Z= 0.948 Chirality : 0.087 0.369 1456 Planarity : 0.006 0.028 1648 Dihedral : 10.612 88.550 3286 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % 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: 0.47 (0.23), residues: 1174 helix: -1.21 (0.44), residues: 95 sheet: 0.80 (0.23), residues: 457 loop : 0.32 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 32 TYR 0.030 0.005 TYR B 103 PHE 0.024 0.004 PHE A 276 TRP 0.020 0.006 TRP B 308 HIS 0.005 0.001 HIS A 521 Details of bonding type rmsd/Z covalent geometry : bond 0.01379 / 0.75 ( 9395) covalent geometry : angle 1.39568 / 0.95 (12744) SS BOND : bond 0.04336 / 2.17 ( 9) SS BOND : angle 2.07281 / 1.36 ( 18) hydrogen bonds : bond 0.16567 / 10.90 ( 332) hydrogen bonds : angle 9.04010 / 6.30 ( 873) link_ALPHA1-2 : bond 0.07253 / 3.82 ( 1) link_ALPHA1-2 : angle 3.58567 / 2.23 ( 3) link_ALPHA1-3 : bond 0.07330 / 3.86 ( 1) link_ALPHA1-3 : angle 3.45177 / 2.31 ( 3) link_ALPHA1-6 : bond 0.05101 / 2.68 ( 1) link_ALPHA1-6 : angle 2.69440 / 1.85 ( 3) link_BETA1-4 : bond 0.06247 / 3.41 ( 6) link_BETA1-4 : angle 3.52250 / 2.09 ( 18) link_NAG-ASN : bond 0.06459 / 3.45 ( 8) link_NAG-ASN : angle 2.15531 / 1.36 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.7852 (ptm) cc_final: 0.7498 (ptp) REVERT: E 52 ASN cc_start: 0.7606 (t0) cc_final: 0.6974 (p0) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1124 time to fit residues: 24.6207 Evaluate side-chains 70 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 100 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105484 restraints weight = 20888.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108415 restraints weight = 11190.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110367 restraints weight = 7176.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111742 restraints weight = 5160.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.112691 restraints weight = 4007.900| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9421 Z= 0.169 Angle : 0.680 13.985 12813 Z= 0.347 Chirality : 0.047 0.155 1456 Planarity : 0.004 0.049 1648 Dihedral : 4.838 27.320 1271 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.72 % Allowed : 6.34 % Favored : 91.94 % 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: 0.54 (0.24), residues: 1174 helix: 0.05 (0.54), residues: 90 sheet: 0.81 (0.22), residues: 465 loop : 0.15 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.015 0.002 TYR A 265 PHE 0.018 0.002 PHE A 276 TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9395) covalent geometry : angle 0.65930 / 0.34 (12744) SS BOND : bond 0.00329 / 0.16 ( 9) SS BOND : angle 2.32365 / 1.38 ( 18) hydrogen bonds : bond 0.04289 / 2.82 ( 332) hydrogen bonds : angle 7.04833 / 4.90 ( 873) link_ALPHA1-2 : bond 0.00583 / 0.31 ( 1) link_ALPHA1-2 : angle 1.70586 / 1.46 ( 3) link_ALPHA1-3 : bond 0.01171 / 0.62 ( 1) link_ALPHA1-3 : angle 1.46951 / 0.88 ( 3) link_ALPHA1-6 : bond 0.00599 / 0.32 ( 1) link_ALPHA1-6 : angle 1.62689 / 1.23 ( 3) link_BETA1-4 : bond 0.01350 / 0.66 ( 6) link_BETA1-4 : angle 3.07163 / 1.90 ( 18) link_NAG-ASN : bond 0.00306 / 0.16 ( 8) link_NAG-ASN : angle 2.00787 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 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: 16 poor density : 83 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8130 (ptm) cc_final: 0.7767 (ptp) REVERT: B 117 MET cc_start: 0.8500 (mmm) cc_final: 0.8218 (tpp) REVERT: B 392 VAL cc_start: 0.8689 (t) cc_final: 0.8458 (p) REVERT: E 52 ASN cc_start: 0.7439 (t0) cc_final: 0.7034 (t0) outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 0.0914 time to fit residues: 12.0663 Evaluate side-chains 64 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN A 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103223 restraints weight = 20994.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106166 restraints weight = 11430.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108142 restraints weight = 7386.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109304 restraints weight = 5351.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110306 restraints weight = 4274.259| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9421 Z= 0.146 Angle : 0.605 13.167 12813 Z= 0.305 Chirality : 0.046 0.190 1456 Planarity : 0.004 0.030 1648 Dihedral : 4.535 27.762 1271 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.50 % Allowed : 7.20 % Favored : 91.30 % 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: 1174 helix: 0.31 (0.56), residues: 89 sheet: 0.79 (0.23), residues: 462 loop : 0.06 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.026 0.001 TYR A 265 PHE 0.014 0.001 PHE A 477 TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9395) covalent geometry : angle 0.59206 / 0.30 (12744) SS BOND : bond 0.00167 / 0.08 ( 9) SS BOND : angle 1.05061 / 0.63 ( 18) hydrogen bonds : bond 0.03630 / 2.36 ( 332) hydrogen bonds : angle 6.48772 / 4.49 ( 873) link_ALPHA1-2 : bond 0.00615 / 0.32 ( 1) link_ALPHA1-2 : angle 1.30311 / 1.01 ( 3) link_ALPHA1-3 : bond 0.00793 / 0.42 ( 1) link_ALPHA1-3 : angle 1.27803 / 0.84 ( 3) link_ALPHA1-6 : bond 0.00686 / 0.36 ( 1) link_ALPHA1-6 : angle 1.38086 / 1.03 ( 3) link_BETA1-4 : bond 0.01225 / 0.60 ( 6) link_BETA1-4 : angle 2.49055 / 1.53 ( 18) link_NAG-ASN : bond 0.00422 / 0.24 ( 8) link_NAG-ASN : angle 1.74679 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8221 (ptm) cc_final: 0.7869 (ptp) REVERT: B 117 MET cc_start: 0.8449 (mmm) cc_final: 0.8232 (tpp) REVERT: B 392 VAL cc_start: 0.8661 (t) cc_final: 0.8416 (p) REVERT: E 111 THR cc_start: 0.7777 (m) cc_final: 0.7495 (p) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.0848 time to fit residues: 8.7038 Evaluate side-chains 59 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.116412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097962 restraints weight = 21607.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100709 restraints weight = 11924.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.102587 restraints weight = 7899.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103859 restraints weight = 5824.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104733 restraints weight = 4653.437| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9421 Z= 0.216 Angle : 0.652 12.046 12813 Z= 0.332 Chirality : 0.047 0.170 1456 Planarity : 0.004 0.038 1648 Dihedral : 4.816 25.167 1271 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.04 % Allowed : 7.84 % 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: 0.21 (0.24), residues: 1174 helix: 0.32 (0.58), residues: 90 sheet: 0.51 (0.23), residues: 461 loop : -0.08 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.018 0.002 TYR A 112 PHE 0.016 0.002 PHE F 107 TRP 0.019 0.002 TRP E 47 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 9395) covalent geometry : angle 0.63761 / 0.33 (12744) SS BOND : bond 0.00369 / 0.18 ( 9) SS BOND : angle 1.19457 / 0.73 ( 18) hydrogen bonds : bond 0.03741 / 2.44 ( 332) hydrogen bonds : angle 6.31435 / 4.37 ( 873) link_ALPHA1-2 : bond 0.00293 / 0.15 ( 1) link_ALPHA1-2 : angle 1.73395 / 1.48 ( 3) link_ALPHA1-3 : bond 0.00591 / 0.31 ( 1) link_ALPHA1-3 : angle 1.23002 / 0.79 ( 3) link_ALPHA1-6 : bond 0.00447 / 0.24 ( 1) link_ALPHA1-6 : angle 1.59453 / 1.17 ( 3) link_BETA1-4 : bond 0.01107 / 0.53 ( 6) link_BETA1-4 : angle 2.62930 / 1.68 ( 18) link_NAG-ASN : bond 0.00443 / 0.22 ( 8) link_NAG-ASN : angle 2.01946 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8361 (ptm) cc_final: 0.8085 (ptp) REVERT: B 94 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7379 (ppp) REVERT: B 110 LEU cc_start: 0.8920 (tp) cc_final: 0.8571 (tt) REVERT: E 111 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7576 (p) REVERT: F 87 SER cc_start: 0.5940 (m) cc_final: 0.5497 (t) REVERT: F 99 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8276 (ttpp) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.0902 time to fit residues: 9.8612 Evaluate side-chains 64 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 383 ASN Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.0970 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.0270 chunk 110 optimal weight: 0.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.118644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099984 restraints weight = 21216.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102783 restraints weight = 11759.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104713 restraints weight = 7784.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105991 restraints weight = 5722.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106756 restraints weight = 4553.611| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9421 Z= 0.113 Angle : 0.552 12.391 12813 Z= 0.277 Chirality : 0.045 0.143 1456 Planarity : 0.003 0.030 1648 Dihedral : 4.391 24.605 1271 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.50 % Allowed : 9.02 % Favored : 89.47 % 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: 0.30 (0.24), residues: 1174 helix: 0.49 (0.58), residues: 90 sheet: 0.67 (0.24), residues: 443 loop : -0.10 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 476 TYR 0.011 0.001 TYR F 59 PHE 0.009 0.001 PHE A 477 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9395) covalent geometry : angle 0.54027 / 0.27 (12744) SS BOND : bond 0.00159 / 0.07 ( 9) SS BOND : angle 0.64148 / 0.39 ( 18) hydrogen bonds : bond 0.03093 / 2.03 ( 332) hydrogen bonds : angle 6.01163 / 4.11 ( 873) link_ALPHA1-2 : bond 0.00589 / 0.31 ( 1) link_ALPHA1-2 : angle 1.41445 / 1.14 ( 3) link_ALPHA1-3 : bond 0.00537 / 0.28 ( 1) link_ALPHA1-3 : angle 1.36221 / 1.04 ( 3) link_ALPHA1-6 : bond 0.00666 / 0.35 ( 1) link_ALPHA1-6 : angle 1.39361 / 1.08 ( 3) link_BETA1-4 : bond 0.01143 / 0.55 ( 6) link_BETA1-4 : angle 2.28902 / 1.43 ( 18) link_NAG-ASN : bond 0.00210 / 0.12 ( 8) link_NAG-ASN : angle 1.61481 / 0.96 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7876 (mtp) cc_final: 0.7674 (mtp) REVERT: A 400 MET cc_start: 0.8358 (ptm) cc_final: 0.8085 (ptp) REVERT: B 94 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7400 (ppp) REVERT: B 110 LEU cc_start: 0.8849 (tp) cc_final: 0.8473 (tt) REVERT: B 392 VAL cc_start: 0.8697 (t) cc_final: 0.8491 (p) REVERT: E 111 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7558 (p) REVERT: F 87 SER cc_start: 0.6206 (m) cc_final: 0.5789 (t) REVERT: F 99 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8252 (ttpp) outliers start: 14 outliers final: 10 residues processed: 66 average time/residue: 0.0945 time to fit residues: 9.1281 Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 0.5980 chunk 108 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 100 optimal weight: 0.0470 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.119673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101035 restraints weight = 21071.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103849 restraints weight = 11733.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105795 restraints weight = 7737.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107080 restraints weight = 5692.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.107927 restraints weight = 4511.631| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9421 Z= 0.107 Angle : 0.529 11.553 12813 Z= 0.266 Chirality : 0.044 0.145 1456 Planarity : 0.003 0.030 1648 Dihedral : 4.158 23.478 1271 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.50 % Allowed : 8.92 % 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: 0.33 (0.24), residues: 1174 helix: 0.64 (0.58), residues: 90 sheet: 0.76 (0.24), residues: 432 loop : -0.15 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 164 TYR 0.009 0.001 TYR F 59 PHE 0.010 0.001 PHE A 477 TRP 0.010 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9395) covalent geometry : angle 0.51802 / 0.26 (12744) SS BOND : bond 0.00160 / 0.07 ( 9) SS BOND : angle 0.54370 / 0.33 ( 18) hydrogen bonds : bond 0.02839 / 1.86 ( 332) hydrogen bonds : angle 5.77831 / 3.95 ( 873) link_ALPHA1-2 : bond 0.00331 / 0.17 ( 1) link_ALPHA1-2 : angle 1.40179 / 1.17 ( 3) link_ALPHA1-3 : bond 0.00460 / 0.24 ( 1) link_ALPHA1-3 : angle 1.34593 / 1.05 ( 3) link_ALPHA1-6 : bond 0.00603 / 0.32 ( 1) link_ALPHA1-6 : angle 1.39239 / 1.09 ( 3) link_BETA1-4 : bond 0.01154 / 0.56 ( 6) link_BETA1-4 : angle 2.24028 / 1.40 ( 18) link_NAG-ASN : bond 0.00202 / 0.12 ( 8) link_NAG-ASN : angle 1.52204 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8295 (ptm) cc_final: 0.8033 (ptp) REVERT: B 94 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7405 (ppp) REVERT: B 117 MET cc_start: 0.8841 (tpp) cc_final: 0.8543 (tpp) REVERT: B 394 MET cc_start: 0.4855 (ppp) cc_final: 0.4614 (ppp) REVERT: E 111 THR cc_start: 0.7986 (m) cc_final: 0.7785 (p) REVERT: F 99 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8261 (ttpp) outliers start: 14 outliers final: 11 residues processed: 66 average time/residue: 0.0882 time to fit residues: 8.5840 Evaluate side-chains 60 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 14 optimal weight: 0.0060 chunk 106 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.101464 restraints weight = 21040.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104543 restraints weight = 12351.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105093 restraints weight = 7293.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106012 restraints weight = 6523.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106128 restraints weight = 6125.655| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9421 Z= 0.121 Angle : 0.527 10.835 12813 Z= 0.265 Chirality : 0.044 0.151 1456 Planarity : 0.003 0.032 1648 Dihedral : 4.133 22.995 1271 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.04 % Allowed : 9.02 % Favored : 88.94 % 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: 0.26 (0.24), residues: 1174 helix: 0.83 (0.59), residues: 90 sheet: 0.54 (0.24), residues: 450 loop : -0.11 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 133 TYR 0.012 0.001 TYR A 112 PHE 0.012 0.001 PHE B 93 TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9395) covalent geometry : angle 0.51575 / 0.26 (12744) SS BOND : bond 0.00185 / 0.09 ( 9) SS BOND : angle 0.55414 / 0.34 ( 18) hydrogen bonds : bond 0.02903 / 1.90 ( 332) hydrogen bonds : angle 5.73364 / 3.93 ( 873) link_ALPHA1-2 : bond 0.00400 / 0.21 ( 1) link_ALPHA1-2 : angle 1.43483 / 1.19 ( 3) link_ALPHA1-3 : bond 0.00485 / 0.26 ( 1) link_ALPHA1-3 : angle 1.36300 / 1.04 ( 3) link_ALPHA1-6 : bond 0.00591 / 0.31 ( 1) link_ALPHA1-6 : angle 1.40912 / 1.11 ( 3) link_BETA1-4 : bond 0.01076 / 0.52 ( 6) link_BETA1-4 : angle 2.19503 / 1.38 ( 18) link_NAG-ASN : bond 0.00186 / 0.10 ( 8) link_NAG-ASN : angle 1.55517 / 0.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8357 (ptm) cc_final: 0.8106 (ptp) REVERT: A 524 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7485 (m-40) REVERT: B 94 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7293 (ppp) REVERT: B 394 MET cc_start: 0.5094 (ppp) cc_final: 0.4849 (ppp) REVERT: F 99 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8221 (ttpp) outliers start: 19 outliers final: 13 residues processed: 62 average time/residue: 0.0951 time to fit residues: 8.5208 Evaluate side-chains 61 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN B 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.114848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096987 restraints weight = 21255.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099609 restraints weight = 12986.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100079 restraints weight = 8091.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100540 restraints weight = 7421.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100661 restraints weight = 7030.271| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 9421 Z= 0.282 Angle : 0.684 10.181 12813 Z= 0.350 Chirality : 0.048 0.165 1456 Planarity : 0.004 0.039 1648 Dihedral : 4.853 22.811 1271 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.93 % Allowed : 9.34 % 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: -0.18 (0.24), residues: 1174 helix: 0.47 (0.58), residues: 90 sheet: 0.25 (0.24), residues: 459 loop : -0.42 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.023 0.002 TYR A 112 PHE 0.021 0.002 PHE B 388 TRP 0.023 0.002 TRP E 47 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.28 ( 9395) covalent geometry : angle 0.67075 / 0.35 (12744) SS BOND : bond 0.00381 / 0.18 ( 9) SS BOND : angle 0.99381 / 0.61 ( 18) hydrogen bonds : bond 0.03863 / 2.51 ( 332) hydrogen bonds : angle 6.24576 / 4.34 ( 873) link_ALPHA1-2 : bond 0.00318 / 0.17 ( 1) link_ALPHA1-2 : angle 1.68637 / 1.40 ( 3) link_ALPHA1-3 : bond 0.00625 / 0.33 ( 1) link_ALPHA1-3 : angle 1.35452 / 0.85 ( 3) link_ALPHA1-6 : bond 0.00464 / 0.24 ( 1) link_ALPHA1-6 : angle 1.65993 / 1.20 ( 3) link_BETA1-4 : bond 0.01022 / 0.49 ( 6) link_BETA1-4 : angle 2.45892 / 1.63 ( 18) link_NAG-ASN : bond 0.00701 / 0.35 ( 8) link_NAG-ASN : angle 2.23142 / 1.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8451 (ptm) cc_final: 0.8243 (ptp) REVERT: A 524 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: B 94 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7474 (ppp) REVERT: B 407 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8541 (tp) REVERT: F 34 ASP cc_start: 0.8824 (t0) cc_final: 0.8546 (t0) REVERT: F 87 SER cc_start: 0.6403 (m) cc_final: 0.5961 (t) outliers start: 18 outliers final: 12 residues processed: 65 average time/residue: 0.0942 time to fit residues: 8.9866 Evaluate side-chains 60 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 95 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.117854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099431 restraints weight = 20976.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102025 restraints weight = 12155.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103804 restraints weight = 8191.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105012 restraints weight = 6173.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105806 restraints weight = 5009.974| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9421 Z= 0.119 Angle : 0.544 11.228 12813 Z= 0.274 Chirality : 0.045 0.152 1456 Planarity : 0.003 0.031 1648 Dihedral : 4.316 21.741 1271 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.72 % Allowed : 9.88 % 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 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: -0.07 (0.24), residues: 1174 helix: 0.62 (0.59), residues: 92 sheet: 0.30 (0.24), residues: 447 loop : -0.34 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.011 0.001 TYR A 112 PHE 0.013 0.001 PHE B 388 TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9395) covalent geometry : angle 0.53360 / 0.27 (12744) SS BOND : bond 0.00174 / 0.08 ( 9) SS BOND : angle 0.70427 / 0.43 ( 18) hydrogen bonds : bond 0.02977 / 1.94 ( 332) hydrogen bonds : angle 5.93552 / 4.07 ( 873) link_ALPHA1-2 : bond 0.00486 / 0.26 ( 1) link_ALPHA1-2 : angle 1.30883 / 1.05 ( 3) link_ALPHA1-3 : bond 0.00435 / 0.23 ( 1) link_ALPHA1-3 : angle 1.49534 / 1.16 ( 3) link_ALPHA1-6 : bond 0.00726 / 0.38 ( 1) link_ALPHA1-6 : angle 1.41412 / 1.10 ( 3) link_BETA1-4 : bond 0.01017 / 0.49 ( 6) link_BETA1-4 : angle 2.08366 / 1.31 ( 18) link_NAG-ASN : bond 0.00208 / 0.11 ( 8) link_NAG-ASN : angle 1.57422 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7231 (pmm) cc_final: 0.6881 (ptt) REVERT: A 400 MET cc_start: 0.8324 (ptm) cc_final: 0.8110 (ptp) REVERT: A 524 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7435 (m-40) REVERT: B 94 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7292 (ppp) REVERT: B 117 MET cc_start: 0.8831 (tpp) cc_final: 0.8473 (tpp) REVERT: B 407 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8474 (tp) REVERT: F 34 ASP cc_start: 0.8626 (t0) cc_final: 0.8329 (t0) outliers start: 16 outliers final: 12 residues processed: 63 average time/residue: 0.0958 time to fit residues: 8.8736 Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.114094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.095961 restraints weight = 20801.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098469 restraints weight = 12076.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100130 restraints weight = 8237.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.101304 restraints weight = 6277.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102086 restraints weight = 5110.139| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9421 Z= 0.197 Angle : 0.607 10.843 12813 Z= 0.307 Chirality : 0.046 0.192 1456 Planarity : 0.004 0.032 1648 Dihedral : 4.546 20.912 1271 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.83 % Allowed : 9.88 % 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: -0.20 (0.24), residues: 1174 helix: 0.70 (0.59), residues: 90 sheet: 0.15 (0.24), residues: 458 loop : -0.40 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.017 0.001 TYR A 112 PHE 0.014 0.001 PHE A 477 TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 9395) covalent geometry : angle 0.59474 / 0.30 (12744) SS BOND : bond 0.00222 / 0.11 ( 9) SS BOND : angle 0.81149 / 0.50 ( 18) hydrogen bonds : bond 0.03447 / 2.25 ( 332) hydrogen bonds : angle 6.09024 / 4.21 ( 873) link_ALPHA1-2 : bond 0.00368 / 0.19 ( 1) link_ALPHA1-2 : angle 1.55483 / 1.31 ( 3) link_ALPHA1-3 : bond 0.00488 / 0.26 ( 1) link_ALPHA1-3 : angle 1.42656 / 0.97 ( 3) link_ALPHA1-6 : bond 0.00500 / 0.26 ( 1) link_ALPHA1-6 : angle 1.51106 / 1.13 ( 3) link_BETA1-4 : bond 0.00991 / 0.47 ( 6) link_BETA1-4 : angle 2.26460 / 1.49 ( 18) link_NAG-ASN : bond 0.00517 / 0.26 ( 8) link_NAG-ASN : angle 1.96419 / 1.17 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7265 (pmm) cc_final: 0.6976 (ptp) REVERT: A 400 MET cc_start: 0.8316 (ptm) cc_final: 0.7956 (ptp) REVERT: A 524 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7307 (m-40) REVERT: B 94 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7310 (ppp) REVERT: B 228 ILE cc_start: 0.9043 (mm) cc_final: 0.8752 (mt) REVERT: F 34 ASP cc_start: 0.8653 (t0) cc_final: 0.8338 (t0) REVERT: F 70 ASP cc_start: 0.6225 (t0) cc_final: 0.6016 (t0) REVERT: F 87 SER cc_start: 0.6334 (m) cc_final: 0.5969 (t) outliers start: 17 outliers final: 12 residues processed: 64 average time/residue: 0.0991 time to fit residues: 9.1578 Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 109 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.117254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098824 restraints weight = 20830.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101383 restraints weight = 12161.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103123 restraints weight = 8248.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.104190 restraints weight = 6241.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105057 restraints weight = 5148.561| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9421 Z= 0.130 Angle : 0.563 11.971 12813 Z= 0.280 Chirality : 0.045 0.152 1456 Planarity : 0.003 0.031 1648 Dihedral : 4.340 20.863 1271 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.61 % Allowed : 10.53 % Favored : 87.86 % 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: -0.19 (0.24), residues: 1174 helix: 0.72 (0.59), residues: 92 sheet: 0.12 (0.24), residues: 450 loop : -0.35 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 143 TYR 0.012 0.001 TYR A 112 PHE 0.012 0.001 PHE B 388 TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9395) covalent geometry : angle 0.55200 / 0.28 (12744) SS BOND : bond 0.00208 / 0.10 ( 9) SS BOND : angle 0.94430 / 0.59 ( 18) hydrogen bonds : bond 0.03055 / 2.01 ( 332) hydrogen bonds : angle 5.91693 / 4.07 ( 873) link_ALPHA1-2 : bond 0.00459 / 0.24 ( 1) link_ALPHA1-2 : angle 1.36687 / 1.12 ( 3) link_ALPHA1-3 : bond 0.00392 / 0.21 ( 1) link_ALPHA1-3 : angle 1.49211 / 1.11 ( 3) link_ALPHA1-6 : bond 0.00601 / 0.32 ( 1) link_ALPHA1-6 : angle 1.39496 / 1.09 ( 3) link_BETA1-4 : bond 0.00988 / 0.47 ( 6) link_BETA1-4 : angle 2.07384 / 1.31 ( 18) link_NAG-ASN : bond 0.00266 / 0.14 ( 8) link_NAG-ASN : angle 1.64701 / 1.01 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.39 seconds wall clock time: 27 minutes 45.58 seconds (1665.58 seconds total)