Starting phenix.real_space_refine on Wed Mar 4 01:10:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d74_27227/03_2026/8d74_27227.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d74_27227/03_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_27227/03_2026/8d74_27227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d74_27227/03_2026/8d74_27227.map" model { file = "/net/cci-nas-00/data/ceres_data/8d74_27227/03_2026/8d74_27227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d74_27227/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.17, per 1000 atoms: 0.23 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: 0.85 Conformation dependent library (CDL) restraints added in 357.1 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: 0.26 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: 1.29 Time building geometry restraints manager: 1.08 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 - 21.71: 5751 21.71 - 43.42: 283 43.42 - 65.13: 69 65.13 - 86.84: 24 86.84 - 108.54: 25 Dihedral angle restraints: 6152 sinusoidal: 2713 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=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" O3 NAG E 1 " ideal model delta sinusoidal sigma weight residual -175.09 -66.55 -108.54 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " ideal model delta sinusoidal sigma weight residual -52.39 55.69 -108.08 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 6149 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 16.068 108.545 3888 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 covalent geometry : bond 0.00269 ( 9897) covalent geometry : angle 0.50729 (13494) SS BOND : bond 0.00597 ( 8) SS BOND : angle 1.29593 ( 16) hydrogen bonds : bond 0.24704 ( 295) hydrogen bonds : angle 7.95604 ( 822) link_BETA1-4 : bond 0.00554 ( 6) link_BETA1-4 : angle 1.89551 ( 18) link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 2.05008 ( 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 : 0.341 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: 0.1249 time to fit residues: 23.7976 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 : 0.279 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4357 r_free = 0.4357 target = 0.189009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138410 restraints weight = 13802.053| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.45 r_work: 0.3705 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9923 Z= 0.141 Angle : 0.620 7.971 13564 Z= 0.300 Chirality : 0.047 0.216 1563 Planarity : 0.004 0.064 1679 Dihedral : 12.831 84.768 1636 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.31 % Allowed : 11.05 % Favored : 85.65 % 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 245 TYR 0.014 0.001 TYR D 80 PHE 0.014 0.001 PHE B 316 TRP 0.007 0.001 TRP B 519 HIS 0.006 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9897) covalent geometry : angle 0.60660 (13494) SS BOND : bond 0.00184 ( 8) SS BOND : angle 0.61126 ( 16) hydrogen bonds : bond 0.04460 ( 295) hydrogen bonds : angle 5.67725 ( 822) link_BETA1-4 : bond 0.00808 ( 6) link_BETA1-4 : angle 1.97420 ( 18) link_NAG-ASN : bond 0.00820 ( 12) link_NAG-ASN : angle 2.24240 ( 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 136 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.376 Fit side-chains REVERT: A 199 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 470 TRP cc_start: 0.7247 (p-90) cc_final: 0.6824 (p-90) REVERT: D 30 ASP cc_start: 0.8284 (m-30) cc_final: 0.7987 (m-30) REVERT: D 48 ILE cc_start: 0.7431 (mm) cc_final: 0.7147 (mm) REVERT: D 67 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7815 (pp) REVERT: D 92 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 178 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8834 (tttm) REVERT: B 381 ARG cc_start: 0.7392 (ttm110) cc_final: 0.6993 (mtp85) REVERT: B 429 GLU cc_start: 0.7488 (pt0) cc_final: 0.6337 (tp30) outliers start: 35 outliers final: 20 residues processed: 127 average time/residue: 0.0904 time to fit residues: 16.4095 Evaluate side-chains 110 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 427 VAL 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: 2.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 256 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.179975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128868 restraints weight = 13482.824| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.40 r_work: 0.3543 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9923 Z= 0.245 Angle : 0.740 7.666 13564 Z= 0.366 Chirality : 0.052 0.298 1563 Planarity : 0.005 0.061 1679 Dihedral : 10.754 79.226 1634 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.34 % Allowed : 13.69 % Favored : 81.96 % 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: -1.91 (0.23), residues: 1153 helix: 2.32 (0.42), residues: 134 sheet: -1.16 (0.23), residues: 457 loop : -2.29 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 72 TYR 0.018 0.002 TYR C 136 PHE 0.022 0.002 PHE D 105 TRP 0.021 0.002 TRP A 457 HIS 0.009 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9897) covalent geometry : angle 0.72425 (13494) SS BOND : bond 0.00465 ( 8) SS BOND : angle 1.20220 ( 16) hydrogen bonds : bond 0.06748 ( 295) hydrogen bonds : angle 5.40826 ( 822) link_BETA1-4 : bond 0.00596 ( 6) link_BETA1-4 : angle 2.30696 ( 18) link_NAG-ASN : bond 0.00958 ( 12) link_NAG-ASN : angle 2.52387 ( 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 142 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: A 367 GLU cc_start: 0.7008 (pm20) cc_final: 0.6176 (pm20) REVERT: D 30 ASP cc_start: 0.8495 (m-30) cc_final: 0.8168 (m-30) REVERT: D 54 ASP cc_start: 0.5167 (m-30) cc_final: 0.4901 (m-30) REVERT: D 67 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 117 ARG cc_start: 0.9141 (ttp-170) cc_final: 0.8855 (ttp-170) REVERT: C 178 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8870 (tttm) REVERT: B 381 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7101 (mtp85) REVERT: B 429 GLU cc_start: 0.7411 (pt0) cc_final: 0.6107 (tp30) outliers start: 46 outliers final: 28 residues processed: 128 average time/residue: 0.0842 time to fit residues: 15.8249 Evaluate side-chains 114 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 235 GLU 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 252 ASP Chi-restraints excluded: chain B residue 137 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 222 CYS 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: 0.5980 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128527 restraints weight = 13682.848| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.43 r_work: 0.3573 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9923 Z= 0.135 Angle : 0.631 12.304 13564 Z= 0.302 Chirality : 0.047 0.230 1563 Planarity : 0.004 0.059 1679 Dihedral : 10.061 75.365 1632 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.59 % Allowed : 16.15 % Favored : 80.26 % 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: -1.54 (0.24), residues: 1153 helix: 3.06 (0.41), residues: 128 sheet: -0.95 (0.23), residues: 459 loop : -2.08 (0.24), residues: 566 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 C 243 TRP 0.009 0.001 TRP A 440 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9897) covalent geometry : angle 0.59332 (13494) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.86966 ( 16) hydrogen bonds : bond 0.05001 ( 295) hydrogen bonds : angle 4.99017 ( 822) link_BETA1-4 : bond 0.01124 ( 6) link_BETA1-4 : angle 2.35647 ( 18) link_NAG-ASN : bond 0.00695 ( 12) link_NAG-ASN : angle 3.88356 ( 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 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8107 (mt-10) REVERT: D 30 ASP cc_start: 0.8439 (m-30) cc_final: 0.8154 (m-30) REVERT: D 54 ASP cc_start: 0.5176 (m-30) cc_final: 0.4925 (m-30) REVERT: C 178 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8914 (tttm) REVERT: B 348 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5169 (pm20) REVERT: B 381 ARG cc_start: 0.7464 (ttm110) cc_final: 0.7064 (mtp85) outliers start: 38 outliers final: 28 residues processed: 123 average time/residue: 0.0928 time to fit residues: 16.2702 Evaluate side-chains 117 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 347 VAL 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 416 ILE 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 144 ILE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 222 CYS 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 285 THR 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 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: 0.9980 chunk 108 optimal weight: 5.9990 chunk 58 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.179418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127864 restraints weight = 13590.241| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.41 r_work: 0.3565 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3179 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= 0.143 Angle : 0.615 8.693 13564 Z= 0.299 Chirality : 0.047 0.231 1563 Planarity : 0.004 0.061 1679 Dihedral : 9.397 70.334 1630 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.72 % Allowed : 15.86 % 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: -1.43 (0.24), residues: 1153 helix: 3.15 (0.41), residues: 128 sheet: -0.90 (0.23), residues: 463 loop : -2.00 (0.24), residues: 562 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 0.009 0.001 PHE D 105 TRP 0.008 0.001 TRP A 457 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9897) covalent geometry : angle 0.59151 (13494) SS BOND : bond 0.00300 ( 8) SS BOND : angle 0.98363 ( 16) hydrogen bonds : bond 0.04869 ( 295) hydrogen bonds : angle 4.89182 ( 822) link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 1.90266 ( 18) link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 2.99228 ( 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 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 367 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: D 30 ASP cc_start: 0.8449 (m-30) cc_final: 0.8158 (m-30) REVERT: D 54 ASP cc_start: 0.5321 (m-30) cc_final: 0.5009 (m-30) REVERT: C 178 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8918 (tttm) REVERT: C 302 TRP cc_start: 0.7970 (t60) cc_final: 0.7570 (t60) REVERT: B 348 GLU cc_start: 0.5725 (OUTLIER) cc_final: 0.4599 (pm20) REVERT: B 381 ARG cc_start: 0.7503 (ttm110) cc_final: 0.7094 (mtp85) REVERT: B 458 ASN cc_start: 0.7412 (t0) cc_final: 0.7051 (t0) outliers start: 50 outliers final: 35 residues processed: 125 average time/residue: 0.0893 time to fit residues: 16.3792 Evaluate side-chains 125 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 346 THR 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 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 444 THR 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 178 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 145 SER 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 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 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: 1.9990 chunk 112 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.178623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128002 restraints weight = 13648.952| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.40 r_work: 0.3532 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9923 Z= 0.196 Angle : 0.696 15.260 13564 Z= 0.336 Chirality : 0.050 0.482 1563 Planarity : 0.005 0.060 1679 Dihedral : 9.125 65.195 1628 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.29 % Allowed : 15.96 % Favored : 78.75 % 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: -1.53 (0.24), residues: 1153 helix: 2.53 (0.43), residues: 134 sheet: -0.89 (0.23), residues: 462 loop : -2.04 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 72 TYR 0.019 0.002 TYR A 334 PHE 0.011 0.001 PHE C 243 TRP 0.016 0.002 TRP A 457 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9897) covalent geometry : angle 0.65327 (13494) SS BOND : bond 0.00373 ( 8) SS BOND : angle 1.26413 ( 16) hydrogen bonds : bond 0.05578 ( 295) hydrogen bonds : angle 4.94804 ( 822) link_BETA1-4 : bond 0.01057 ( 6) link_BETA1-4 : angle 2.14622 ( 18) link_NAG-ASN : bond 0.00646 ( 12) link_NAG-ASN : angle 4.41362 ( 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 151 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 95 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7458 (tt0) cc_final: 0.7024 (pt0) REVERT: A 324 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6553 (m-30) REVERT: D 30 ASP cc_start: 0.8505 (m-30) cc_final: 0.8214 (m-30) REVERT: C 117 ARG cc_start: 0.9113 (ttp-170) cc_final: 0.8844 (ttp-170) REVERT: C 178 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8902 (tttm) REVERT: B 348 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.4105 (pm20) REVERT: B 381 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7078 (mtp85) REVERT: B 458 ASN cc_start: 0.7471 (t0) cc_final: 0.7109 (t0) outliers start: 56 outliers final: 42 residues processed: 137 average time/residue: 0.0915 time to fit residues: 18.3874 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 258 ASN Chi-restraints excluded: chain A residue 324 ASP 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 444 THR 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 178 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 145 SER 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 222 CYS 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 297 VAL 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 425 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: 3.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.180009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129752 restraints weight = 13591.233| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.40 r_work: 0.3556 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9923 Z= 0.138 Angle : 0.627 11.358 13564 Z= 0.304 Chirality : 0.047 0.253 1563 Planarity : 0.004 0.062 1679 Dihedral : 8.525 59.375 1627 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.24 % Rotamer: Outliers : 4.82 % Allowed : 16.53 % Favored : 78.66 % 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: 2.71 (0.43), residues: 134 sheet: -0.84 (0.23), residues: 465 loop : -1.98 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 117 TYR 0.016 0.001 TYR A 334 PHE 0.007 0.001 PHE C 243 TRP 0.009 0.001 TRP B 172 HIS 0.004 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9897) covalent geometry : angle 0.59764 (13494) SS BOND : bond 0.00253 ( 8) SS BOND : angle 1.10028 ( 16) hydrogen bonds : bond 0.04860 ( 295) hydrogen bonds : angle 4.79791 ( 822) link_BETA1-4 : bond 0.00706 ( 6) link_BETA1-4 : angle 1.95844 ( 18) link_NAG-ASN : bond 0.00510 ( 12) link_NAG-ASN : angle 3.45272 ( 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 144 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7387 (tt0) cc_final: 0.6975 (pt0) REVERT: A 324 ASP cc_start: 0.6755 (m-30) cc_final: 0.6541 (m-30) REVERT: D 30 ASP cc_start: 0.8517 (m-30) cc_final: 0.8194 (m-30) REVERT: C 178 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8911 (tttm) REVERT: B 381 ARG cc_start: 0.7496 (ttm110) cc_final: 0.7092 (mtp85) REVERT: B 458 ASN cc_start: 0.7559 (t0) cc_final: 0.7254 (t0) outliers start: 51 outliers final: 42 residues processed: 130 average time/residue: 0.0897 time to fit residues: 16.8099 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 : 0.367 ------------------------------------------------------------------------------- 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 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 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 444 THR 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 178 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 222 CYS 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 372 VAL Chi-restraints excluded: chain B residue 425 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.176579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125232 restraints weight = 13563.876| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.40 r_work: 0.3527 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9923 Z= 0.182 Angle : 0.676 14.921 13564 Z= 0.326 Chirality : 0.049 0.342 1563 Planarity : 0.004 0.061 1679 Dihedral : 8.364 59.647 1627 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.37 % Rotamer: Outliers : 5.10 % Allowed : 16.34 % 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: -1.45 (0.24), residues: 1153 helix: 2.59 (0.43), residues: 134 sheet: -0.85 (0.24), residues: 461 loop : -1.97 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.019 0.002 TYR A 334 PHE 0.009 0.001 PHE A 214 TRP 0.012 0.001 TRP A 457 HIS 0.005 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9897) covalent geometry : angle 0.63520 (13494) SS BOND : bond 0.00399 ( 8) SS BOND : angle 1.28594 ( 16) hydrogen bonds : bond 0.05305 ( 295) hydrogen bonds : angle 4.85180 ( 822) link_BETA1-4 : bond 0.00882 ( 6) link_BETA1-4 : angle 2.01331 ( 18) link_NAG-ASN : bond 0.00526 ( 12) link_NAG-ASN : angle 4.23751 ( 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 149 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7391 (tt0) cc_final: 0.7016 (pt0) REVERT: A 347 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7521 (m) REVERT: D 30 ASP cc_start: 0.8486 (m-30) cc_final: 0.8168 (m-30) REVERT: B 381 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7102 (mtp85) REVERT: B 458 ASN cc_start: 0.7652 (t0) cc_final: 0.7309 (t0) outliers start: 54 outliers final: 43 residues processed: 134 average time/residue: 0.0915 time to fit residues: 17.5925 Evaluate side-chains 137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 285 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 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 444 THR 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 153 VAL Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 222 CYS 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 349 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN D 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.181075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131031 restraints weight = 13483.606| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.40 r_work: 0.3573 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9923 Z= 0.121 Angle : 0.625 12.504 13564 Z= 0.302 Chirality : 0.046 0.258 1563 Planarity : 0.004 0.062 1679 Dihedral : 7.964 57.581 1627 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 3.49 % Allowed : 17.94 % 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: 2.86 (0.43), residues: 134 sheet: -0.65 (0.24), residues: 452 loop : -1.95 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 163 TYR 0.012 0.001 TYR D 80 PHE 0.006 0.001 PHE A 297 TRP 0.010 0.001 TRP B 172 HIS 0.004 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9897) covalent geometry : angle 0.59143 (13494) SS BOND : bond 0.00375 ( 8) SS BOND : angle 1.00308 ( 16) hydrogen bonds : bond 0.04431 ( 295) hydrogen bonds : angle 4.74738 ( 822) link_BETA1-4 : bond 0.00736 ( 6) link_BETA1-4 : angle 1.96990 ( 18) link_NAG-ASN : bond 0.00498 ( 12) link_NAG-ASN : angle 3.68131 ( 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 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7364 (tt0) cc_final: 0.6944 (pt0) REVERT: A 324 ASP cc_start: 0.6615 (m-30) cc_final: 0.6354 (m-30) REVERT: D 30 ASP cc_start: 0.8511 (m-30) cc_final: 0.8189 (m-30) REVERT: B 381 ARG cc_start: 0.7520 (ttm110) cc_final: 0.7099 (mtp85) REVERT: B 458 ASN cc_start: 0.7514 (t0) cc_final: 0.7188 (t0) outliers start: 37 outliers final: 31 residues processed: 123 average time/residue: 0.0938 time to fit residues: 16.7079 Evaluate side-chains 123 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 444 THR 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 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 380 VAL 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: 1.9990 chunk 88 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.177768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127439 restraints weight = 13491.278| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.37 r_work: 0.3526 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9923 Z= 0.207 Angle : 0.684 12.369 13564 Z= 0.334 Chirality : 0.049 0.252 1563 Planarity : 0.005 0.061 1679 Dihedral : 7.996 58.180 1626 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.89 % Favored : 92.02 % Rotamer: Outliers : 3.78 % Allowed : 17.85 % Favored : 78.38 % 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: -1.38 (0.24), residues: 1153 helix: 2.62 (0.43), residues: 134 sheet: -0.79 (0.24), residues: 468 loop : -1.94 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 245 TYR 0.017 0.002 TYR D 80 PHE 0.009 0.001 PHE B 328 TRP 0.010 0.002 TRP A 470 HIS 0.006 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9897) covalent geometry : angle 0.65402 (13494) SS BOND : bond 0.00502 ( 8) SS BOND : angle 1.62043 ( 16) hydrogen bonds : bond 0.05420 ( 295) hydrogen bonds : angle 4.87238 ( 822) link_BETA1-4 : bond 0.00624 ( 6) link_BETA1-4 : angle 1.93695 ( 18) link_NAG-ASN : bond 0.00548 ( 12) link_NAG-ASN : angle 3.62382 ( 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 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7412 (tt0) cc_final: 0.7002 (pt0) REVERT: A 336 ILE cc_start: 0.8520 (pt) cc_final: 0.8310 (pt) REVERT: D 30 ASP cc_start: 0.8514 (m-30) cc_final: 0.8216 (m-30) REVERT: B 381 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7081 (mtp85) REVERT: B 458 ASN cc_start: 0.7633 (t0) cc_final: 0.7280 (t0) outliers start: 40 outliers final: 33 residues processed: 122 average time/residue: 0.0934 time to fit residues: 16.4326 Evaluate side-chains 122 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 444 THR 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 184 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 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 522 TRP 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: 3.9990 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.180122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130073 restraints weight = 13607.772| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.37 r_work: 0.3560 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9923 Z= 0.130 Angle : 0.628 11.336 13564 Z= 0.308 Chirality : 0.046 0.252 1563 Planarity : 0.004 0.058 1679 Dihedral : 7.745 59.471 1626 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.40 % Allowed : 18.32 % Favored : 78.28 % 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: 2.81 (0.43), residues: 134 sheet: -0.71 (0.24), residues: 459 loop : -1.88 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.020 0.001 TYR B 505 PHE 0.006 0.001 PHE C 243 TRP 0.011 0.001 TRP B 172 HIS 0.003 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9897) covalent geometry : angle 0.60052 (13494) SS BOND : bond 0.00321 ( 8) SS BOND : angle 1.17645 ( 16) hydrogen bonds : bond 0.04598 ( 295) hydrogen bonds : angle 4.71630 ( 822) link_BETA1-4 : bond 0.00646 ( 6) link_BETA1-4 : angle 1.87661 ( 18) link_NAG-ASN : bond 0.00502 ( 12) link_NAG-ASN : angle 3.34010 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3760.46 seconds wall clock time: 64 minutes 37.01 seconds (3877.01 seconds total)