Starting phenix.real_space_refine on Thu Feb 13 21:43:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ujc_20796/02_2025/6ujc_20796.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ujc_20796/02_2025/6ujc_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_20796/02_2025/6ujc_20796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ujc_20796/02_2025/6ujc_20796.map" model { file = "/net/cci-nas-00/data/ceres_data/6ujc_20796/02_2025/6ujc_20796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ujc_20796/02_2025/6ujc_20796.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' MG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.05, per 1000 atoms: 0.66 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: 2.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.31 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: 3.42 Time building geometry restraints manager: 3.14 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 - 21.51: 5669 21.51 - 43.01: 107 43.01 - 64.52: 30 64.52 - 86.02: 19 86.02 - 107.53: 7 Dihedral angle restraints: 5832 sinusoidal: 2437 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 5829 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.420 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 0.080 9395 Z= 0.904 Angle : 1.396 8.544 12744 Z= 0.948 Chirality : 0.087 0.369 1456 Planarity : 0.006 0.028 1648 Dihedral : 11.400 107.525 3635 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 TRP 0.020 0.006 TRP B 308 HIS 0.005 0.001 HIS A 521 PHE 0.024 0.004 PHE A 276 TYR 0.030 0.005 TYR B 103 ARG 0.005 0.001 ARG F 32 *********************** 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 : 1.004 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: 0.2769 time to fit residues: 59.2765 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 : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 0.0050 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.123219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105428 restraints weight = 20841.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108331 restraints weight = 11219.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.110317 restraints weight = 7227.812| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9395 Z= 0.242 Angle : 0.651 14.618 12744 Z= 0.336 Chirality : 0.048 0.164 1456 Planarity : 0.004 0.056 1648 Dihedral : 7.593 86.237 1620 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 6.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1174 helix: 0.02 (0.53), residues: 90 sheet: 0.80 (0.22), residues: 465 loop : 0.14 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.002 0.001 HIS B 118 PHE 0.017 0.002 PHE A 276 TYR 0.015 0.002 TYR A 265 ARG 0.007 0.001 ARG A 476 *********************** 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: 17 poor density : 82 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8202 (ptm) cc_final: 0.7810 (ptp) REVERT: B 117 MET cc_start: 0.8463 (mmm) cc_final: 0.8189 (tpp) REVERT: B 392 VAL cc_start: 0.8700 (t) cc_final: 0.8463 (p) REVERT: E 52 ASN cc_start: 0.7395 (t0) cc_final: 0.6947 (t0) REVERT: F 100 GLN cc_start: 0.8543 (pp30) cc_final: 0.8340 (pp30) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.2323 time to fit residues: 30.1247 Evaluate side-chains 67 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 5 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3864 r_free = 0.3864 target = 0.119485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101253 restraints weight = 21184.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.104070 restraints weight = 11732.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105996 restraints weight = 7719.899| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9395 Z= 0.274 Angle : 0.621 12.850 12744 Z= 0.318 Chirality : 0.047 0.209 1456 Planarity : 0.004 0.040 1648 Dihedral : 6.468 66.751 1620 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.61 % Allowed : 7.20 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1174 helix: 0.29 (0.56), residues: 89 sheet: 0.59 (0.23), residues: 459 loop : -0.01 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.004 0.001 HIS B 166 PHE 0.014 0.001 PHE A 477 TYR 0.021 0.002 TYR A 265 ARG 0.005 0.001 ARG A 398 *********************** 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 78 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8352 (ptm) cc_final: 0.7998 (ptp) REVERT: B 94 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7244 (ppp) REVERT: B 110 LEU cc_start: 0.8923 (tp) cc_final: 0.8593 (tt) REVERT: B 271 VAL cc_start: 0.8869 (t) cc_final: 0.8657 (p) REVERT: E 52 ASN cc_start: 0.7454 (t0) cc_final: 0.7093 (t0) REVERT: E 111 THR cc_start: 0.7842 (m) cc_final: 0.7615 (p) REVERT: F 21 MET cc_start: 0.7446 (ptp) cc_final: 0.7153 (ptp) REVERT: F 87 SER cc_start: 0.6082 (m) cc_final: 0.5670 (t) REVERT: F 100 GLN cc_start: 0.8667 (pp30) cc_final: 0.8437 (pp30) outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.2206 time to fit residues: 22.6492 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 : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain B residue 94 MET 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 Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096688 restraints weight = 21191.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099748 restraints weight = 12093.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100327 restraints weight = 7450.773| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9395 Z= 0.409 Angle : 0.692 11.407 12744 Z= 0.358 Chirality : 0.049 0.257 1456 Planarity : 0.005 0.050 1648 Dihedral : 6.301 53.383 1620 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.36 % Allowed : 7.84 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1174 helix: 0.13 (0.57), residues: 90 sheet: 0.30 (0.24), residues: 464 loop : -0.29 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 47 HIS 0.006 0.001 HIS B 280 PHE 0.017 0.002 PHE A 94 TYR 0.023 0.002 TYR A 112 ARG 0.005 0.001 ARG B 86 *********************** 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 81 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8534 (ptm) cc_final: 0.8266 (ptp) REVERT: B 94 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7331 (ppp) REVERT: B 110 LEU cc_start: 0.8897 (tp) cc_final: 0.8522 (tt) REVERT: E 52 ASN cc_start: 0.7618 (t0) cc_final: 0.7380 (t0) REVERT: E 111 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7548 (p) REVERT: F 21 MET cc_start: 0.7858 (ptp) cc_final: 0.7512 (ptp) outliers start: 22 outliers final: 13 residues processed: 75 average time/residue: 0.2411 time to fit residues: 26.3305 Evaluate side-chains 62 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 383 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.114819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097274 restraints weight = 21242.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099764 restraints weight = 12823.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100737 restraints weight = 8312.814| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 9395 Z= 0.372 Angle : 0.648 11.286 12744 Z= 0.335 Chirality : 0.048 0.261 1456 Planarity : 0.004 0.040 1648 Dihedral : 6.056 48.849 1620 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.69 % Allowed : 8.49 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1174 helix: 0.15 (0.57), residues: 90 sheet: 0.31 (0.25), residues: 432 loop : -0.50 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.004 0.001 HIS B 166 PHE 0.013 0.001 PHE A 477 TYR 0.020 0.002 TYR A 112 ARG 0.003 0.000 ARG A 168 *********************** 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 80 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7998 (mtp) cc_final: 0.7757 (mtp) REVERT: A 400 MET cc_start: 0.8444 (ptm) cc_final: 0.8191 (ptp) REVERT: A 524 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7513 (m-40) REVERT: B 94 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7166 (ppp) REVERT: B 110 LEU cc_start: 0.8901 (tp) cc_final: 0.8538 (tt) REVERT: E 52 ASN cc_start: 0.7490 (t0) cc_final: 0.7280 (t0) REVERT: E 111 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7620 (p) REVERT: F 21 MET cc_start: 0.7955 (ptp) cc_final: 0.7708 (ptp) outliers start: 25 outliers final: 17 residues processed: 73 average time/residue: 0.2167 time to fit residues: 23.1460 Evaluate side-chains 69 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 A residue 524 ASN Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL 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 E residue 113 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.115944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097625 restraints weight = 20967.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100139 restraints weight = 12268.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101912 restraints weight = 8336.170| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9395 Z= 0.217 Angle : 0.565 11.321 12744 Z= 0.289 Chirality : 0.046 0.256 1456 Planarity : 0.004 0.030 1648 Dihedral : 5.633 45.861 1620 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.36 % Allowed : 9.67 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1174 helix: 0.38 (0.58), residues: 90 sheet: 0.21 (0.25), residues: 437 loop : -0.43 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE A 477 TYR 0.014 0.001 TYR A 112 ARG 0.002 0.000 ARG B 164 *********************** 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 75 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8380 (ptm) cc_final: 0.8145 (ptp) REVERT: A 524 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: B 94 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7157 (ppp) REVERT: B 110 LEU cc_start: 0.8873 (tp) cc_final: 0.8510 (tt) REVERT: B 383 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7390 (t0) REVERT: B 394 MET cc_start: 0.4806 (ppp) cc_final: 0.4461 (ppp) REVERT: E 52 ASN cc_start: 0.7574 (t0) cc_final: 0.7286 (t0) REVERT: E 111 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7520 (p) outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.2052 time to fit residues: 20.7022 Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 319 THR Chi-restraints excluded: chain B residue 350 VAL 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 Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.117584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098745 restraints weight = 21008.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101495 restraints weight = 11930.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103350 restraints weight = 7957.681| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9395 Z= 0.165 Angle : 0.535 11.173 12744 Z= 0.273 Chirality : 0.046 0.244 1456 Planarity : 0.003 0.031 1648 Dihedral : 5.334 44.325 1620 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.04 % Allowed : 9.88 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1174 helix: 0.56 (0.59), residues: 90 sheet: 0.14 (0.24), residues: 443 loop : -0.45 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 PHE 0.016 0.001 PHE B 388 TYR 0.013 0.001 TYR F 59 ARG 0.002 0.000 ARG A 476 *********************** 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 74 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8405 (ptm) cc_final: 0.8176 (ptp) REVERT: B 94 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7166 (ppp) REVERT: B 110 LEU cc_start: 0.8875 (tp) cc_final: 0.8496 (tt) REVERT: B 394 MET cc_start: 0.4832 (ppp) cc_final: 0.4465 (ppp) REVERT: E 52 ASN cc_start: 0.7581 (t0) cc_final: 0.7276 (t0) REVERT: E 111 THR cc_start: 0.7759 (m) cc_final: 0.7490 (p) outliers start: 19 outliers final: 12 residues processed: 67 average time/residue: 0.2350 time to fit residues: 22.2625 Evaluate side-chains 63 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TRP 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 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 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.117100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099700 restraints weight = 21330.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102380 restraints weight = 12542.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102887 restraints weight = 7879.404| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9395 Z= 0.196 Angle : 0.537 11.386 12744 Z= 0.274 Chirality : 0.045 0.227 1456 Planarity : 0.003 0.029 1648 Dihedral : 5.184 41.971 1620 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.26 % Allowed : 10.10 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1174 helix: 0.55 (0.59), residues: 92 sheet: 0.16 (0.24), residues: 451 loop : -0.47 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 PHE 0.011 0.001 PHE B 388 TYR 0.013 0.001 TYR F 59 ARG 0.003 0.000 ARG A 398 *********************** 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 74 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8440 (ptm) cc_final: 0.8218 (ptp) REVERT: A 524 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7434 (m-40) REVERT: B 94 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7387 (ppp) REVERT: B 110 LEU cc_start: 0.8907 (tp) cc_final: 0.8522 (tt) REVERT: B 394 MET cc_start: 0.5007 (ppp) cc_final: 0.4675 (ppp) REVERT: B 407 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8501 (tp) REVERT: E 52 ASN cc_start: 0.7561 (t0) cc_final: 0.7247 (t0) REVERT: E 111 THR cc_start: 0.7772 (m) cc_final: 0.7520 (p) outliers start: 21 outliers final: 17 residues processed: 70 average time/residue: 0.2205 time to fit residues: 22.3584 Evaluate side-chains 69 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 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 97 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.116496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098077 restraints weight = 20899.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100666 restraints weight = 12202.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102435 restraints weight = 8296.850| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9395 Z= 0.219 Angle : 0.548 11.061 12744 Z= 0.280 Chirality : 0.046 0.213 1456 Planarity : 0.004 0.030 1648 Dihedral : 5.156 40.587 1620 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.36 % Allowed : 10.10 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1174 helix: 0.60 (0.59), residues: 92 sheet: 0.14 (0.24), residues: 442 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 PHE 0.010 0.001 PHE A 477 TYR 0.014 0.001 TYR F 59 ARG 0.002 0.000 ARG B 143 *********************** 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 76 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.7734 (mmm) cc_final: 0.7452 (mtt) REVERT: A 400 MET cc_start: 0.8407 (ptm) cc_final: 0.8048 (ptp) REVERT: A 524 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7458 (m-40) REVERT: B 94 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7389 (ppp) REVERT: B 110 LEU cc_start: 0.8903 (tp) cc_final: 0.8502 (tt) REVERT: B 228 ILE cc_start: 0.9014 (mm) cc_final: 0.8697 (mt) REVERT: E 52 ASN cc_start: 0.7582 (t0) cc_final: 0.7271 (t0) REVERT: E 111 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7507 (p) outliers start: 22 outliers final: 16 residues processed: 71 average time/residue: 0.2079 time to fit residues: 21.8485 Evaluate side-chains 67 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 97 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.117963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099642 restraints weight = 21211.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102244 restraints weight = 12322.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104052 restraints weight = 8346.010| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9395 Z= 0.165 Angle : 0.530 11.777 12744 Z= 0.267 Chirality : 0.045 0.203 1456 Planarity : 0.003 0.030 1648 Dihedral : 4.976 41.050 1620 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 10.74 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1174 helix: 0.66 (0.59), residues: 92 sheet: 0.15 (0.24), residues: 455 loop : -0.46 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.002 0.001 HIS B 63 PHE 0.011 0.001 PHE A 477 TYR 0.016 0.001 TYR F 59 ARG 0.003 0.000 ARG B 143 ********************** 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 67 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 MET cc_start: 0.7704 (mmm) cc_final: 0.7464 (mtt) REVERT: A 400 MET cc_start: 0.8392 (ptm) cc_final: 0.8049 (ptp) REVERT: A 524 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7395 (m-40) REVERT: B 94 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7413 (ppp) REVERT: B 110 LEU cc_start: 0.8956 (tp) cc_final: 0.8525 (tt) REVERT: B 117 MET cc_start: 0.8837 (tpp) cc_final: 0.8426 (mpp) REVERT: B 228 ILE cc_start: 0.8994 (mm) cc_final: 0.8657 (mt) REVERT: E 52 ASN cc_start: 0.7620 (t0) cc_final: 0.7383 (t0) REVERT: E 111 THR cc_start: 0.7963 (m) cc_final: 0.7726 (p) outliers start: 17 outliers final: 14 residues processed: 62 average time/residue: 0.2174 time to fit residues: 19.9245 Evaluate side-chains 65 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 97 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 99 PHE Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 4 optimal weight: 0.0000 chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.117288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098522 restraints weight = 21127.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101291 restraints weight = 11917.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103206 restraints weight = 7932.157| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9395 Z= 0.193 Angle : 0.535 11.614 12744 Z= 0.271 Chirality : 0.045 0.191 1456 Planarity : 0.003 0.030 1648 Dihedral : 4.941 41.409 1620 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.04 % Allowed : 10.53 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1174 helix: 0.71 (0.60), residues: 92 sheet: 0.23 (0.24), residues: 452 loop : -0.44 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.002 0.001 HIS A 113 PHE 0.012 0.001 PHE A 477 TYR 0.014 0.001 TYR F 59 ARG 0.003 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.82 seconds wall clock time: 50 minutes 11.97 seconds (3011.97 seconds total)