Starting phenix.real_space_refine on Thu Jul 2 18:49:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.map" model { file = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2026/8d74_27227.cif" } resolution = 3.03 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= -0.000 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 6150 2.51 5 N 1611 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9639 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 365} Chain: "D" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1416 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1607 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 20, 'TRANS': 178} Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3197 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 378} Chain breaks: 1 Chain: "E" 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: "F" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.78, per 1000 atoms: 0.18 Number of scatterers: 9639 At special positions: 0 Unit cell: (97.75, 141.95, 183.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1843 8.00 N 1611 7.00 C 6150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 511 " distance=2.05 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 390 " " NAG A 703 " - " ASN A 157 " " NAG A 704 " - " ASN A 383 " " NAG A 705 " - " ASN A 379 " " NAG C 401 " - " ASN C 142 " " NAG E 1 " - " ASN A 227 " " NAG F 1 " - " ASN C 190 " " NAG G 1 " - " ASN B 407 " " NAG H 1 " - " ASN B 426 " " NAG I 1 " - " ASN B 303 " " NAG J 1 " - " ASN B 243 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 248.9 milliseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 24 sheets defined 13.3% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.843A pdb=" N SER A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.534A pdb=" N ASN A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 43 removed outlier: 4.367A pdb=" N LEU D 16 " --> pdb=" O HIS D 12 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 97 Processing helix chain 'D' and resid 102 through 130 removed outlier: 3.621A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 183 removed outlier: 4.032A pdb=" N GLU D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.926A pdb=" N VAL B 163 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.732A pdb=" N CYS B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 214 " --> pdb=" O LEU B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 214' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 8.237A pdb=" N LYS A 221 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.253A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 205 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 4.253A pdb=" N ASN A 157 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 201 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.038A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.645A pdb=" N ARG A 300 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 removed outlier: 3.672A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.129A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 403 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 367 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 399 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 371 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.109A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 474 removed outlier: 4.109A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS A 458 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 117 Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 211 through 214 Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 258 Processing sheet with id=AB7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AB8, first strand: chain 'B' and resid 141 through 147 removed outlier: 3.968A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 156 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP B 157 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B 201 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.544A pdb=" N TYR B 223 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 173 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.518A pdb=" N CYS B 270 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 259 through 262 removed outlier: 6.313A pdb=" N LYS B 259 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 330 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 261 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 279 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 337 through 342 removed outlier: 5.180A pdb=" N GLN B 338 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN B 354 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.580A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.938A pdb=" N HIS B 454 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE B 439 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER B 452 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 464 through 471 removed outlier: 3.884A pdb=" N ILE B 484 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS B 466 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 482 " --> pdb=" O CYS B 466 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG B 480 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 470 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 478 " --> pdb=" O ILE B 470 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 822 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: 1.65 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3033 1.35 - 1.48: 2598 1.48 - 1.60: 4219 1.60 - 1.73: 0 1.73 - 1.85: 47 Bond restraints: 9897 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 9892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 13222 1.57 - 3.14: 237 3.14 - 4.71: 30 4.71 - 6.29: 4 6.29 - 7.86: 1 Bond angle restraints: 13494 Sorted by residual: angle pdb=" C TRP A 164 " pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.46e+00 angle pdb=" N CYS B 511 " pdb=" CA CYS B 511 " pdb=" C CYS B 511 " ideal model delta sigma weight residual 108.96 112.97 -4.01 1.49e+00 4.50e-01 7.25e+00 angle pdb=" C TYR B 502 " pdb=" N THR B 503 " pdb=" CA THR B 503 " ideal model delta sigma weight residual 121.54 125.92 -4.38 1.91e+00 2.74e-01 5.27e+00 angle pdb=" C CYS B 511 " pdb=" N SER B 512 " pdb=" CA SER B 512 " ideal model delta sigma weight residual 122.16 125.15 -2.99 1.32e+00 5.74e-01 5.12e+00 angle pdb=" CA LEU B 184 " pdb=" CB LEU B 184 " pdb=" CG LEU B 184 " ideal model delta sigma weight residual 116.30 124.16 -7.86 3.50e+00 8.16e-02 5.04e+00 ... (remaining 13489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 5305 17.09 - 34.17: 381 34.17 - 51.26: 65 51.26 - 68.35: 13 68.35 - 85.43: 10 Dihedral angle restraints: 5774 sinusoidal: 2335 harmonic: 3439 Sorted by residual: dihedral pdb=" CA THR B 447 " pdb=" C THR B 447 " pdb=" N ALA B 448 " pdb=" CA ALA B 448 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CB CYS B 466 " pdb=" SG CYS B 466 " pdb=" SG CYS B 511 " pdb=" CB CYS B 511 " ideal model delta sinusoidal sigma weight residual 93.00 63.50 29.50 1 1.00e+01 1.00e-02 1.24e+01 dihedral pdb=" CA HIS D 97 " pdb=" C HIS D 97 " pdb=" N PHE D 98 " pdb=" CA PHE D 98 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1282 0.052 - 0.103: 219 0.103 - 0.155: 56 0.155 - 0.206: 5 0.206 - 0.258: 1 Chirality restraints: 1563 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 426 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 131 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 142 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.69e-01 ... (remaining 1560 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 501 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 445 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 446 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 446 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 446 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 337 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 338 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.017 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 494 2.73 - 3.27: 8975 3.27 - 3.81: 14828 3.81 - 4.36: 16953 4.36 - 4.90: 30339 Nonbonded interactions: 71589 Sorted by model distance: nonbonded pdb=" OG1 THR A 341 " pdb=" O TYR A 344 " model vdw 2.184 3.040 nonbonded pdb=" O LEU A 364 " pdb=" O3 NAG A 704 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR B 409 " pdb=" O7 NAG G 1 " model vdw 2.230 3.040 nonbonded pdb=" O GLY B 283 " pdb=" OG1 THR B 285 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 371 " pdb=" O LEU A 397 " model vdw 2.309 3.040 ... (remaining 71584 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.003 0.044 9923 Z= 0.136 Angle : 0.523 7.858 13564 Z= 0.260 Chirality : 0.043 0.258 1563 Planarity : 0.004 0.066 1679 Dihedral : 12.344 85.432 3510 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.85 % Allowed : 7.55 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -2.86 (0.21), residues: 1153 helix: 1.82 (0.39), residues: 127 sheet: -1.67 (0.23), residues: 420 loop : -2.99 (0.20), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 384 TYR 0.007 0.001 TYR B 502 PHE 0.014 0.001 PHE A 433 TRP 0.004 0.000 TRP A 333 HIS 0.002 0.000 HIS B 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 9897) covalent geometry : angle 0.50729 / 0.26 (13494) SS BOND : bond 0.00597 / 0.20 ( 8) SS BOND : angle 1.29593 / 2.23 ( 16) hydrogen bonds : bond 0.24704 / 16.62 ( 295) hydrogen bonds : angle 7.95604 / 5.52 ( 822) link_BETA1-4 : bond 0.00554 / 0.30 ( 6) link_BETA1-4 : angle 1.89551 / 1.02 ( 18) link_NAG-ASN : bond 0.00355 / 0.37 ( 12) link_NAG-ASN : angle 2.05008 / 1.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 428 MET cc_start: 0.3301 (ppp) cc_final: 0.3033 (pmm) REVERT: D 30 ASP cc_start: 0.7934 (m-30) cc_final: 0.7598 (m-30) REVERT: D 67 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6835 (pp) REVERT: B 429 GLU cc_start: 0.7363 (pt0) cc_final: 0.6215 (tp30) outliers start: 9 outliers final: 7 residues processed: 145 average time/residue: 0.1023 time to fit residues: 20.0190 Evaluate side-chains 102 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 511 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0370 chunk 100 optimal weight: 0.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN A 376 HIS A 485 ASN D 12 HIS D 42 GLN D 76 ASN D 107 GLN D 122 GLN D 145 ASN D 163 GLN D 182 HIS C 255 GLN B 226 ASN B 313 ASN B 390 ASN B 403 GLN B 458 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.189316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.138795 restraints weight = 13826.357| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.45 r_work: 0.3709 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9923 Z= 0.141 Angle : 0.580 7.260 13564 Z= 0.289 Chirality : 0.047 0.296 1563 Planarity : 0.004 0.064 1679 Dihedral : 4.311 43.885 1258 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.12 % Allowed : 11.05 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.96 (0.23), residues: 1153 helix: 2.97 (0.40), residues: 128 sheet: -1.26 (0.23), residues: 431 loop : -2.36 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 220 TYR 0.014 0.001 TYR D 80 PHE 0.013 0.001 PHE B 316 TRP 0.007 0.001 TRP A 440 HIS 0.005 0.001 HIS D 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9897) covalent geometry : angle 0.56679 / 0.29 (13494) SS BOND : bond 0.00135 / 0.07 ( 8) SS BOND : angle 0.55745 / 0.46 ( 16) hydrogen bonds : bond 0.04551 / 3.14 ( 295) hydrogen bonds : angle 5.71943 / 3.90 ( 822) link_BETA1-4 : bond 0.00548 / 0.35 ( 6) link_BETA1-4 : angle 2.00531 / 1.23 ( 18) link_NAG-ASN : bond 0.00741 / 0.43 ( 12) link_NAG-ASN : angle 1.99917 / 1.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 30 ASP cc_start: 0.8287 (m-30) cc_final: 0.7989 (m-30) REVERT: D 48 ILE cc_start: 0.7452 (mm) cc_final: 0.7162 (mm) REVERT: D 67 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7763 (pp) REVERT: D 92 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8582 (tm-30) REVERT: C 178 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8808 (tttm) REVERT: B 381 ARG cc_start: 0.7394 (ttm110) cc_final: 0.6992 (mtp85) REVERT: B 429 GLU cc_start: 0.7491 (pt0) cc_final: 0.6342 (tp30) outliers start: 33 outliers final: 19 residues processed: 125 average time/residue: 0.0868 time to fit residues: 15.5958 Evaluate side-chains 112 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0170 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 226 HIS ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.180167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128367 restraints weight = 13570.524| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.44 r_work: 0.3552 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9923 Z= 0.222 Angle : 0.692 9.505 13564 Z= 0.345 Chirality : 0.050 0.224 1563 Planarity : 0.005 0.061 1679 Dihedral : 5.218 44.179 1256 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.25 % Allowed : 13.69 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.76 (0.23), residues: 1153 helix: 2.76 (0.41), residues: 128 sheet: -1.06 (0.23), residues: 454 loop : -2.22 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 72 TYR 0.017 0.002 TYR D 80 PHE 0.019 0.002 PHE D 105 TRP 0.018 0.002 TRP A 457 HIS 0.008 0.001 HIS D 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 ( 9897) covalent geometry : angle 0.66905 / 0.34 (13494) SS BOND : bond 0.00253 / 0.15 ( 8) SS BOND : angle 1.09321 / 0.88 ( 16) hydrogen bonds : bond 0.06250 / 4.38 ( 295) hydrogen bonds : angle 5.33077 / 3.65 ( 822) link_BETA1-4 : bond 0.00472 / 0.29 ( 6) link_BETA1-4 : angle 1.95014 / 1.12 ( 18) link_NAG-ASN : bond 0.00726 / 0.70 ( 12) link_NAG-ASN : angle 3.18471 / 2.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: D 30 ASP cc_start: 0.8427 (m-30) cc_final: 0.8116 (m-30) REVERT: D 54 ASP cc_start: 0.5236 (m-30) cc_final: 0.5013 (m-30) REVERT: D 67 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (pp) REVERT: C 178 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8911 (tttm) REVERT: B 381 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7100 (mtp85) REVERT: B 429 GLU cc_start: 0.7464 (pt0) cc_final: 0.6142 (tp30) outliers start: 45 outliers final: 28 residues processed: 135 average time/residue: 0.0940 time to fit residues: 18.1095 Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.180994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129520 restraints weight = 13696.597| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.45 r_work: 0.3585 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9923 Z= 0.135 Angle : 0.612 11.345 13564 Z= 0.297 Chirality : 0.047 0.231 1563 Planarity : 0.004 0.058 1679 Dihedral : 4.796 31.352 1254 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.59 % Allowed : 15.68 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.50 (0.24), residues: 1153 helix: 3.08 (0.41), residues: 128 sheet: -0.89 (0.23), residues: 456 loop : -2.09 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 221 TYR 0.020 0.001 TYR A 334 PHE 0.008 0.001 PHE D 105 TRP 0.009 0.001 TRP A 440 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9897) covalent geometry : angle 0.57982 / 0.29 (13494) SS BOND : bond 0.00341 / 0.36 ( 8) SS BOND : angle 0.77899 / 0.55 ( 16) hydrogen bonds : bond 0.04882 / 3.42 ( 295) hydrogen bonds : angle 5.00925 / 3.44 ( 822) link_BETA1-4 : bond 0.00666 / 0.43 ( 6) link_BETA1-4 : angle 1.86467 / 0.99 ( 18) link_NAG-ASN : bond 0.00550 / 0.54 ( 12) link_NAG-ASN : angle 3.61141 / 2.21 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: D 30 ASP cc_start: 0.8421 (m-30) cc_final: 0.8130 (m-30) REVERT: D 54 ASP cc_start: 0.5064 (m-30) cc_final: 0.4842 (m-30) REVERT: B 381 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7073 (mtp85) REVERT: B 429 GLU cc_start: 0.7521 (pt0) cc_final: 0.6221 (tp30) outliers start: 38 outliers final: 28 residues processed: 123 average time/residue: 0.0860 time to fit residues: 14.9985 Evaluate side-chains 117 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.0570 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 139 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 = 0.4289 r_free = 0.4289 target = 0.181958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130744 restraints weight = 13620.318| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.41 r_work: 0.3600 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9923 Z= 0.112 Angle : 0.563 7.853 13564 Z= 0.277 Chirality : 0.045 0.238 1563 Planarity : 0.004 0.060 1679 Dihedral : 4.545 31.650 1252 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.44 % Allowed : 15.49 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.28 (0.24), residues: 1153 helix: 3.32 (0.41), residues: 128 sheet: -0.77 (0.23), residues: 460 loop : -1.94 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 25 TYR 0.020 0.001 TYR A 334 PHE 0.008 0.001 PHE D 105 TRP 0.008 0.001 TRP B 172 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9897) covalent geometry : angle 0.54499 / 0.27 (13494) SS BOND : bond 0.00231 / 0.23 ( 8) SS BOND : angle 0.71229 / 0.50 ( 16) hydrogen bonds : bond 0.04310 / 3.02 ( 295) hydrogen bonds : angle 4.71912 / 3.23 ( 822) link_BETA1-4 : bond 0.00552 / 0.35 ( 6) link_BETA1-4 : angle 1.80189 / 1.01 ( 18) link_NAG-ASN : bond 0.00479 / 0.52 ( 12) link_NAG-ASN : angle 2.51940 / 1.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: D 30 ASP cc_start: 0.8424 (m-30) cc_final: 0.8150 (m-30) REVERT: D 54 ASP cc_start: 0.5114 (m-30) cc_final: 0.4886 (m-30) REVERT: C 302 TRP cc_start: 0.7923 (t60) cc_final: 0.7602 (t60) REVERT: B 381 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7085 (mtp85) REVERT: B 429 GLU cc_start: 0.7529 (pt0) cc_final: 0.6219 (tp30) outliers start: 47 outliers final: 36 residues processed: 127 average time/residue: 0.0764 time to fit residues: 14.0495 Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.178570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127799 restraints weight = 13685.177| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.40 r_work: 0.3530 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9923 Z= 0.220 Angle : 0.699 14.476 13564 Z= 0.342 Chirality : 0.050 0.227 1563 Planarity : 0.005 0.060 1679 Dihedral : 5.084 31.198 1252 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.44 % Allowed : 16.15 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.55 (0.24), residues: 1153 helix: 2.45 (0.42), residues: 134 sheet: -0.87 (0.24), residues: 460 loop : -2.07 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 72 TYR 0.019 0.002 TYR D 80 PHE 0.013 0.002 PHE D 105 TRP 0.019 0.002 TRP A 457 HIS 0.012 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 ( 9897) covalent geometry : angle 0.67682 / 0.34 (13494) SS BOND : bond 0.00409 / 0.37 ( 8) SS BOND : angle 1.23223 / 0.87 ( 16) hydrogen bonds : bond 0.05796 / 4.08 ( 295) hydrogen bonds : angle 5.01983 / 3.42 ( 822) link_BETA1-4 : bond 0.00648 / 0.37 ( 6) link_BETA1-4 : angle 2.29423 / 1.80 ( 18) link_NAG-ASN : bond 0.00564 / 0.62 ( 12) link_NAG-ASN : angle 3.02107 / 2.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: A 336 ILE cc_start: 0.8671 (pt) cc_final: 0.8459 (pt) REVERT: A 367 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: D 30 ASP cc_start: 0.8523 (m-30) cc_final: 0.8228 (m-30) REVERT: B 348 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.4132 (pm20) REVERT: B 381 ARG cc_start: 0.7518 (ttm110) cc_final: 0.7088 (mtp85) REVERT: B 429 GLU cc_start: 0.7470 (pt0) cc_final: 0.6161 (tp30) outliers start: 47 outliers final: 35 residues processed: 133 average time/residue: 0.0821 time to fit residues: 15.7795 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 CYS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.181638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131410 restraints weight = 13633.278| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.39 r_work: 0.3579 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9923 Z= 0.118 Angle : 0.591 8.303 13564 Z= 0.289 Chirality : 0.046 0.259 1563 Planarity : 0.004 0.057 1679 Dihedral : 4.659 22.665 1249 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.06 % Allowed : 17.09 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.32 (0.24), residues: 1153 helix: 2.83 (0.43), residues: 134 sheet: -0.71 (0.24), residues: 467 loop : -1.99 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 25 TYR 0.019 0.001 TYR A 334 PHE 0.007 0.001 PHE C 243 TRP 0.010 0.001 TRP A 197 HIS 0.007 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9897) covalent geometry : angle 0.56997 / 0.28 (13494) SS BOND : bond 0.00260 / 0.27 ( 8) SS BOND : angle 0.82681 / 0.56 ( 16) hydrogen bonds : bond 0.04547 / 3.19 ( 295) hydrogen bonds : angle 4.69652 / 3.20 ( 822) link_BETA1-4 : bond 0.00465 / 0.30 ( 6) link_BETA1-4 : angle 1.85928 / 1.00 ( 18) link_NAG-ASN : bond 0.00492 / 0.51 ( 12) link_NAG-ASN : angle 2.81797 / 1.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 ILE cc_start: 0.8670 (pt) cc_final: 0.8464 (pt) REVERT: A 367 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: A 482 LEU cc_start: 0.7148 (mm) cc_final: 0.6785 (mt) REVERT: D 30 ASP cc_start: 0.8491 (m-30) cc_final: 0.8196 (m-30) REVERT: C 302 TRP cc_start: 0.7929 (t60) cc_final: 0.7722 (t60) REVERT: B 348 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: B 381 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7113 (mtp85) REVERT: B 429 GLU cc_start: 0.7505 (pt0) cc_final: 0.6210 (tp30) outliers start: 43 outliers final: 35 residues processed: 128 average time/residue: 0.0699 time to fit residues: 13.0725 Evaluate side-chains 122 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 85 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.180173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129964 restraints weight = 13545.665| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.36 r_work: 0.3558 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9923 Z= 0.156 Angle : 0.606 8.701 13564 Z= 0.300 Chirality : 0.047 0.229 1563 Planarity : 0.004 0.057 1679 Dihedral : 4.767 23.733 1249 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.82 % Allowed : 16.15 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.35 (0.24), residues: 1153 helix: 2.77 (0.43), residues: 134 sheet: -0.77 (0.24), residues: 467 loop : -1.96 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.018 0.001 TYR A 334 PHE 0.008 0.001 PHE C 243 TRP 0.011 0.001 TRP A 457 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9897) covalent geometry : angle 0.58984 / 0.30 (13494) SS BOND : bond 0.00445 / 0.47 ( 8) SS BOND : angle 1.21006 / 0.82 ( 16) hydrogen bonds : bond 0.04895 / 3.45 ( 295) hydrogen bonds : angle 4.69372 / 3.19 ( 822) link_BETA1-4 : bond 0.00501 / 0.30 ( 6) link_BETA1-4 : angle 1.79906 / 0.94 ( 18) link_NAG-ASN : bond 0.00539 / 0.55 ( 12) link_NAG-ASN : angle 2.36708 / 1.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 88 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7433 (tt0) cc_final: 0.7001 (pt0) REVERT: A 336 ILE cc_start: 0.8619 (pt) cc_final: 0.8413 (pt) REVERT: A 367 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: D 30 ASP cc_start: 0.8512 (m-30) cc_final: 0.8210 (m-30) REVERT: C 302 TRP cc_start: 0.7979 (t60) cc_final: 0.7761 (t60) REVERT: B 348 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.5407 (pm20) REVERT: B 381 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7130 (mtp85) REVERT: B 429 GLU cc_start: 0.7524 (pt0) cc_final: 0.6171 (tp30) outliers start: 51 outliers final: 41 residues processed: 127 average time/residue: 0.0882 time to fit residues: 16.3341 Evaluate side-chains 133 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 9.9990 chunk 99 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.178865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128695 restraints weight = 13487.838| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.34 r_work: 0.3542 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9923 Z= 0.184 Angle : 0.649 13.857 13564 Z= 0.318 Chirality : 0.048 0.227 1563 Planarity : 0.004 0.057 1679 Dihedral : 4.949 26.080 1249 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.91 % Allowed : 16.05 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.42 (0.24), residues: 1153 helix: 2.65 (0.43), residues: 134 sheet: -0.83 (0.24), residues: 467 loop : -1.98 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.017 0.002 TYR D 80 PHE 0.009 0.001 PHE C 243 TRP 0.012 0.001 TRP A 457 HIS 0.005 0.001 HIS D 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 9897) covalent geometry : angle 0.63392 / 0.32 (13494) SS BOND : bond 0.00341 / 0.31 ( 8) SS BOND : angle 1.28337 / 0.87 ( 16) hydrogen bonds : bond 0.05253 / 3.70 ( 295) hydrogen bonds : angle 4.81006 / 3.27 ( 822) link_BETA1-4 : bond 0.00530 / 0.32 ( 6) link_BETA1-4 : angle 1.82353 / 0.95 ( 18) link_NAG-ASN : bond 0.00526 / 0.52 ( 12) link_NAG-ASN : angle 2.34712 / 1.69 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7399 (tt0) cc_final: 0.6981 (pt0) REVERT: A 336 ILE cc_start: 0.8624 (pt) cc_final: 0.8412 (pt) REVERT: A 367 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: D 30 ASP cc_start: 0.8508 (m-30) cc_final: 0.8189 (m-30) REVERT: B 348 GLU cc_start: 0.5541 (OUTLIER) cc_final: 0.5247 (pm20) REVERT: B 381 ARG cc_start: 0.7492 (ttm110) cc_final: 0.7085 (mtp85) REVERT: B 429 GLU cc_start: 0.7603 (pt0) cc_final: 0.7390 (pm20) outliers start: 52 outliers final: 44 residues processed: 138 average time/residue: 0.0907 time to fit residues: 17.9289 Evaluate side-chains 141 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.179237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129180 restraints weight = 13512.311| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.36 r_work: 0.3548 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9923 Z= 0.155 Angle : 0.632 14.308 13564 Z= 0.310 Chirality : 0.047 0.231 1563 Planarity : 0.004 0.057 1679 Dihedral : 4.889 26.438 1249 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.53 % Allowed : 16.43 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.36 (0.24), residues: 1153 helix: 2.70 (0.43), residues: 134 sheet: -0.79 (0.24), residues: 467 loop : -1.94 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.018 0.001 TYR A 334 PHE 0.008 0.001 PHE C 243 TRP 0.010 0.001 TRP B 172 HIS 0.006 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 9897) covalent geometry : angle 0.61761 / 0.31 (13494) SS BOND : bond 0.00324 / 0.32 ( 8) SS BOND : angle 1.11040 / 0.76 ( 16) hydrogen bonds : bond 0.04929 / 3.48 ( 295) hydrogen bonds : angle 4.76059 / 3.23 ( 822) link_BETA1-4 : bond 0.00517 / 0.31 ( 6) link_BETA1-4 : angle 1.79450 / 0.94 ( 18) link_NAG-ASN : bond 0.00507 / 0.51 ( 12) link_NAG-ASN : angle 2.29450 / 1.69 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7397 (tt0) cc_final: 0.6983 (pt0) REVERT: A 336 ILE cc_start: 0.8605 (pt) cc_final: 0.8385 (pt) REVERT: D 30 ASP cc_start: 0.8513 (m-30) cc_final: 0.8198 (m-30) REVERT: B 205 TRP cc_start: 0.7381 (t60) cc_final: 0.7169 (t60) REVERT: B 348 GLU cc_start: 0.5463 (OUTLIER) cc_final: 0.5217 (pm20) REVERT: B 381 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7110 (mtp85) outliers start: 48 outliers final: 41 residues processed: 132 average time/residue: 0.0841 time to fit residues: 16.2066 Evaluate side-chains 136 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.177652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126120 restraints weight = 13667.506| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.43 r_work: 0.3553 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9923 Z= 0.134 Angle : 0.624 14.073 13564 Z= 0.304 Chirality : 0.047 0.234 1563 Planarity : 0.004 0.058 1679 Dihedral : 4.837 27.160 1249 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.06 % Allowed : 17.37 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % 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: -1.26 (0.24), residues: 1153 helix: 2.79 (0.43), residues: 134 sheet: -0.66 (0.24), residues: 458 loop : -1.93 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.018 0.001 TYR A 334 PHE 0.007 0.001 PHE C 243 TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9897) covalent geometry : angle 0.60919 / 0.30 (13494) SS BOND : bond 0.00345 / 0.36 ( 8) SS BOND : angle 1.33648 / 0.88 ( 16) hydrogen bonds : bond 0.04643 / 3.27 ( 295) hydrogen bonds : angle 4.68010 / 3.18 ( 822) link_BETA1-4 : bond 0.00536 / 0.32 ( 6) link_BETA1-4 : angle 1.77973 / 0.94 ( 18) link_NAG-ASN : bond 0.00530 / 0.54 ( 12) link_NAG-ASN : angle 2.31616 / 1.72 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3349.94 seconds wall clock time: 57 minutes 47.78 seconds (3467.78 seconds total)