Starting phenix.real_space_refine on Sun Jul 27 22:11:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d74_27227/07_2025/8d74_27227.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d74_27227/07_2025/8d74_27227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2025/8d74_27227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2025/8d74_27227.map" model { file = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2025/8d74_27227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d74_27227/07_2025/8d74_27227.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 14.79, per 1000 atoms: 1.53 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: 2.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.25 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: 3.13 Time building geometry restraints manager: 3.41 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: 5.820 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 35.460 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- 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 : 5.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.000 TRP A 333 HIS 0.002 0.000 HIS B 528 PHE 0.014 0.001 PHE A 433 TYR 0.007 0.001 TYR B 502 ARG 0.002 0.000 ARG B 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 2.05008 ( 36) link_BETA1-4 : bond 0.00554 ( 6) link_BETA1-4 : angle 1.89551 ( 18) hydrogen bonds : bond 0.24704 ( 295) hydrogen bonds : angle 7.95604 ( 822) SS BOND : bond 0.00597 ( 8) SS BOND : angle 1.29593 ( 16) covalent geometry : bond 0.00269 ( 9897) covalent geometry : angle 0.50729 (13494) *********************** 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 : 1.441 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: 0.2878 time to fit residues: 56.0612 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 : 1.135 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 255 GLN B 166 HIS B 226 ASN B 313 ASN B 321 ASN B 390 ASN B 403 GLN B 458 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.184180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132528 restraints weight = 13654.455| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.46 r_work: 0.3624 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9923 Z= 0.207 Angle : 0.668 8.572 13564 Z= 0.330 Chirality : 0.051 0.355 1563 Planarity : 0.005 0.065 1679 Dihedral : 13.240 90.692 1636 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.49 % Allowed : 11.33 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.23), residues: 1153 helix: 2.39 (0.41), residues: 134 sheet: -1.30 (0.23), residues: 435 loop : -2.47 (0.22), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.011 0.001 HIS A 226 PHE 0.014 0.002 PHE D 105 TYR 0.017 0.002 TYR D 80 ARG 0.005 0.001 ARG C 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 12) link_NAG-ASN : angle 2.58057 ( 36) link_BETA1-4 : bond 0.00891 ( 6) link_BETA1-4 : angle 1.99663 ( 18) hydrogen bonds : bond 0.05703 ( 295) hydrogen bonds : angle 5.84502 ( 822) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.81866 ( 16) covalent geometry : bond 0.00483 ( 9897) covalent geometry : angle 0.65193 (13494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7984 (mt-10) REVERT: D 30 ASP cc_start: 0.8328 (m-30) cc_final: 0.8042 (m-30) REVERT: D 48 ILE cc_start: 0.7492 (mm) cc_final: 0.7224 (mm) REVERT: D 67 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8047 (pp) REVERT: C 178 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8828 (tttm) REVERT: B 381 ARG cc_start: 0.7508 (ttm110) cc_final: 0.7046 (mtp85) REVERT: B 429 GLU cc_start: 0.7470 (pt0) cc_final: 0.6313 (tp30) outliers start: 37 outliers final: 22 residues processed: 125 average time/residue: 0.2171 time to fit residues: 38.5752 Evaluate side-chains 118 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain C residue 160 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 150 THR Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 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 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 110 optimal weight: 0.0050 chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** 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 = 0.4327 r_free = 0.4327 target = 0.186048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134877 restraints weight = 13839.570| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.48 r_work: 0.3662 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9923 Z= 0.105 Angle : 0.572 8.832 13564 Z= 0.274 Chirality : 0.045 0.224 1563 Planarity : 0.004 0.060 1679 Dihedral : 10.996 80.060 1634 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.40 % Allowed : 12.56 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.24), residues: 1153 helix: 3.25 (0.41), residues: 128 sheet: -0.91 (0.23), residues: 443 loop : -2.17 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.003 0.000 HIS C 256 PHE 0.009 0.001 PHE B 464 TYR 0.011 0.001 TYR D 80 ARG 0.002 0.000 ARG C 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 12) link_NAG-ASN : angle 2.16723 ( 36) link_BETA1-4 : bond 0.00539 ( 6) link_BETA1-4 : angle 1.94072 ( 18) hydrogen bonds : bond 0.04400 ( 295) hydrogen bonds : angle 5.19447 ( 822) SS BOND : bond 0.00102 ( 8) SS BOND : angle 0.57570 ( 16) covalent geometry : bond 0.00219 ( 9897) covalent geometry : angle 0.55740 (13494) *********************** 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 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7941 (mt-10) REVERT: A 336 ILE cc_start: 0.8571 (pt) cc_final: 0.8350 (pt) REVERT: D 30 ASP cc_start: 0.8337 (m-30) cc_final: 0.8044 (m-30) REVERT: D 67 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8084 (pp) REVERT: C 178 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8861 (tttm) REVERT: C 269 ASP cc_start: 0.7422 (t0) cc_final: 0.7196 (t0) REVERT: B 381 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7043 (mtp85) REVERT: B 429 GLU cc_start: 0.7522 (pt0) cc_final: 0.6286 (tp30) outliers start: 36 outliers final: 26 residues processed: 124 average time/residue: 0.2144 time to fit residues: 38.3094 Evaluate side-chains 119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 164 CYS 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 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 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 90 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 360 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.183479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132814 restraints weight = 13488.597| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.41 r_work: 0.3602 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9923 Z= 0.158 Angle : 0.631 10.404 13564 Z= 0.303 Chirality : 0.047 0.349 1563 Planarity : 0.004 0.060 1679 Dihedral : 10.072 78.462 1634 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.15 % Allowed : 14.45 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1153 helix: 3.15 (0.41), residues: 128 sheet: -0.93 (0.23), residues: 461 loop : -2.03 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 302 HIS 0.006 0.001 HIS D 174 PHE 0.011 0.001 PHE D 105 TYR 0.015 0.001 TYR D 80 ARG 0.004 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 12) link_NAG-ASN : angle 3.46499 ( 36) link_BETA1-4 : bond 0.00865 ( 6) link_BETA1-4 : angle 2.23844 ( 18) hydrogen bonds : bond 0.04860 ( 295) hydrogen bonds : angle 4.95272 ( 822) SS BOND : bond 0.00287 ( 8) SS BOND : angle 0.81375 ( 16) covalent geometry : bond 0.00365 ( 9897) covalent geometry : angle 0.60023 (13494) *********************** 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 135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7952 (mt-10) REVERT: D 30 ASP cc_start: 0.8450 (m-30) cc_final: 0.8143 (m-30) REVERT: D 54 ASP cc_start: 0.5011 (m-30) cc_final: 0.4811 (m-30) REVERT: D 67 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8300 (pp) REVERT: C 178 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8880 (tttm) REVERT: C 218 ASN cc_start: 0.7893 (m110) cc_final: 0.7673 (m110) REVERT: B 184 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7613 (tm) REVERT: B 381 ARG cc_start: 0.7468 (ttm110) cc_final: 0.7058 (mtp85) REVERT: B 429 GLU cc_start: 0.7461 (pt0) cc_final: 0.6150 (tp30) outliers start: 44 outliers final: 33 residues processed: 124 average time/residue: 0.2190 time to fit residues: 38.4459 Evaluate side-chains 121 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 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 459 VAL Chi-restraints excluded: chain A residue 466 CYS 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 C residue 285 ASN Chi-restraints excluded: chain B residue 144 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.183272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132760 restraints weight = 13539.659| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.41 r_work: 0.3604 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9923 Z= 0.134 Angle : 0.592 7.842 13564 Z= 0.286 Chirality : 0.046 0.222 1563 Planarity : 0.004 0.060 1679 Dihedral : 9.470 69.685 1634 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.15 % Allowed : 15.20 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1153 helix: 3.22 (0.41), residues: 128 sheet: -0.77 (0.23), residues: 456 loop : -2.01 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 457 HIS 0.007 0.001 HIS B 190 PHE 0.008 0.001 PHE D 105 TYR 0.014 0.001 TYR D 80 ARG 0.002 0.000 ARG C 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 12) link_NAG-ASN : angle 2.75459 ( 36) link_BETA1-4 : bond 0.00640 ( 6) link_BETA1-4 : angle 1.94934 ( 18) hydrogen bonds : bond 0.04627 ( 295) hydrogen bonds : angle 4.81415 ( 822) SS BOND : bond 0.00381 ( 8) SS BOND : angle 0.87350 ( 16) covalent geometry : bond 0.00310 ( 9897) covalent geometry : angle 0.57075 (13494) *********************** 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 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 88 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 ASP cc_start: 0.8438 (m-30) cc_final: 0.8128 (m-30) REVERT: D 54 ASP cc_start: 0.4942 (m-30) cc_final: 0.4739 (m-30) REVERT: C 178 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8890 (tttm) REVERT: C 218 ASN cc_start: 0.7896 (m110) cc_final: 0.7677 (m110) REVERT: C 269 ASP cc_start: 0.7629 (t0) cc_final: 0.7364 (t0) REVERT: B 184 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7626 (tm) REVERT: B 381 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7047 (mtp85) REVERT: B 429 GLU cc_start: 0.7492 (pt0) cc_final: 0.6159 (tp30) outliers start: 44 outliers final: 34 residues processed: 122 average time/residue: 0.2036 time to fit residues: 36.0258 Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain A residue 263 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 444 THR 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 56 MET Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 178 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 149 SER 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 241 VAL 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 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.178932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129231 restraints weight = 13274.884| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.34 r_work: 0.3536 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9923 Z= 0.192 Angle : 0.655 8.146 13564 Z= 0.322 Chirality : 0.049 0.226 1563 Planarity : 0.005 0.060 1679 Dihedral : 9.000 63.145 1632 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.00 % Allowed : 14.45 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.24), residues: 1153 helix: 2.52 (0.42), residues: 134 sheet: -0.94 (0.23), residues: 462 loop : -2.07 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 457 HIS 0.007 0.001 HIS D 174 PHE 0.013 0.002 PHE D 105 TYR 0.017 0.002 TYR D 80 ARG 0.005 0.001 ARG C 163 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 12) link_NAG-ASN : angle 2.56568 ( 36) link_BETA1-4 : bond 0.00627 ( 6) link_BETA1-4 : angle 2.02924 ( 18) hydrogen bonds : bond 0.05470 ( 295) hydrogen bonds : angle 4.91511 ( 822) SS BOND : bond 0.00252 ( 8) SS BOND : angle 1.12461 ( 16) covalent geometry : bond 0.00462 ( 9897) covalent geometry : angle 0.63756 (13494) *********************** 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 150 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 97 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7415 (tt0) cc_final: 0.6993 (pt0) REVERT: A 324 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: D 30 ASP cc_start: 0.8488 (m-30) cc_final: 0.8158 (m-30) REVERT: C 178 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8900 (tttm) REVERT: C 218 ASN cc_start: 0.8014 (m110) cc_final: 0.7772 (m110) REVERT: C 269 ASP cc_start: 0.7918 (t0) cc_final: 0.7657 (t0) REVERT: C 302 TRP cc_start: 0.7959 (t60) cc_final: 0.7520 (t60) REVERT: B 381 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7087 (mtp85) outliers start: 53 outliers final: 39 residues processed: 139 average time/residue: 0.2027 time to fit residues: 40.4529 Evaluate side-chains 127 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 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 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 144 LEU 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 241 VAL 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 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 6 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 80 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.180555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130166 restraints weight = 13611.063| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.39 r_work: 0.3562 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9923 Z= 0.155 Angle : 0.653 15.442 13564 Z= 0.312 Chirality : 0.047 0.331 1563 Planarity : 0.004 0.058 1679 Dihedral : 8.556 59.295 1627 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.63 % Allowed : 15.49 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1153 helix: 2.65 (0.43), residues: 134 sheet: -0.87 (0.23), residues: 464 loop : -2.01 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 172 HIS 0.004 0.001 HIS C 256 PHE 0.008 0.001 PHE D 105 TYR 0.015 0.001 TYR D 80 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 12) link_NAG-ASN : angle 4.43728 ( 36) link_BETA1-4 : bond 0.00874 ( 6) link_BETA1-4 : angle 2.11394 ( 18) hydrogen bonds : bond 0.04997 ( 295) hydrogen bonds : angle 4.81797 ( 822) SS BOND : bond 0.00380 ( 8) SS BOND : angle 1.35424 ( 16) covalent geometry : bond 0.00364 ( 9897) covalent geometry : angle 0.60636 (13494) *********************** 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 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 85 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7422 (tt0) cc_final: 0.6995 (pt0) REVERT: A 324 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: D 30 ASP cc_start: 0.8489 (m-30) cc_final: 0.8155 (m-30) REVERT: C 178 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8874 (tttm) REVERT: C 218 ASN cc_start: 0.8017 (m110) cc_final: 0.7750 (m110) REVERT: C 269 ASP cc_start: 0.7832 (t0) cc_final: 0.7571 (t0) REVERT: C 302 TRP cc_start: 0.7938 (t60) cc_final: 0.7462 (t60) REVERT: B 381 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7069 (mtp85) outliers start: 49 outliers final: 39 residues processed: 123 average time/residue: 0.2307 time to fit residues: 41.5403 Evaluate side-chains 124 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 346 THR 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 459 VAL Chi-restraints excluded: chain A residue 466 CYS 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 144 LEU 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 241 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 101 optimal weight: 0.0470 chunk 105 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.178037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126532 restraints weight = 13657.480| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.42 r_work: 0.3547 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9923 Z= 0.151 Angle : 0.630 11.489 13564 Z= 0.306 Chirality : 0.047 0.239 1563 Planarity : 0.004 0.058 1679 Dihedral : 8.080 58.181 1627 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.72 % Allowed : 15.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1153 helix: 2.69 (0.42), residues: 134 sheet: -0.80 (0.23), residues: 465 loop : -1.97 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 172 HIS 0.005 0.001 HIS A 226 PHE 0.008 0.001 PHE C 243 TYR 0.015 0.001 TYR D 80 ARG 0.003 0.000 ARG C 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 3.43392 ( 36) link_BETA1-4 : bond 0.00657 ( 6) link_BETA1-4 : angle 2.00538 ( 18) hydrogen bonds : bond 0.04884 ( 295) hydrogen bonds : angle 4.74876 ( 822) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.24777 ( 16) covalent geometry : bond 0.00355 ( 9897) covalent geometry : angle 0.60020 (13494) *********************** 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 141 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7390 (tt0) cc_final: 0.7008 (pt0) REVERT: D 30 ASP cc_start: 0.8461 (m-30) cc_final: 0.8125 (m-30) REVERT: C 269 ASP cc_start: 0.7812 (t0) cc_final: 0.7552 (t0) REVERT: C 302 TRP cc_start: 0.7975 (t60) cc_final: 0.7517 (t60) REVERT: B 381 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7157 (mtp85) outliers start: 50 outliers final: 42 residues processed: 128 average time/residue: 0.2243 time to fit residues: 43.4693 Evaluate side-chains 128 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 86 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 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 252 ASP Chi-restraints excluded: chain B residue 144 LEU 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 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 380 VAL Chi-restraints excluded: chain B residue 425 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.177484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127167 restraints weight = 13476.113| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.36 r_work: 0.3518 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9923 Z= 0.218 Angle : 0.709 14.153 13564 Z= 0.346 Chirality : 0.050 0.260 1563 Planarity : 0.005 0.058 1679 Dihedral : 8.126 58.463 1627 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 4.15 % Allowed : 15.86 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1153 helix: 2.39 (0.42), residues: 134 sheet: -0.95 (0.23), residues: 461 loop : -1.99 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 457 HIS 0.007 0.001 HIS D 174 PHE 0.012 0.001 PHE B 328 TYR 0.019 0.002 TYR D 80 ARG 0.005 0.001 ARG A 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 12) link_NAG-ASN : angle 3.33499 ( 36) link_BETA1-4 : bond 0.00667 ( 6) link_BETA1-4 : angle 2.01922 ( 18) hydrogen bonds : bond 0.05721 ( 295) hydrogen bonds : angle 4.94203 ( 822) SS BOND : bond 0.00415 ( 8) SS BOND : angle 1.46843 ( 16) covalent geometry : bond 0.00529 ( 9897) covalent geometry : angle 0.68422 (13494) *********************** 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 137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7432 (tt0) cc_final: 0.7018 (pt0) REVERT: A 324 ASP cc_start: 0.6942 (m-30) cc_final: 0.6691 (m-30) REVERT: D 30 ASP cc_start: 0.8523 (m-30) cc_final: 0.8275 (m-30) REVERT: C 269 ASP cc_start: 0.7940 (t0) cc_final: 0.7712 (t0) REVERT: B 381 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7089 (mtp85) outliers start: 44 outliers final: 40 residues processed: 128 average time/residue: 0.2517 time to fit residues: 45.8661 Evaluate side-chains 129 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 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 252 ASP Chi-restraints excluded: chain B residue 144 LEU 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 284 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 425 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 531 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 88 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.179532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129458 restraints weight = 13531.854| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.37 r_work: 0.3549 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9923 Z= 0.142 Angle : 0.654 14.401 13564 Z= 0.316 Chirality : 0.047 0.251 1563 Planarity : 0.004 0.055 1679 Dihedral : 7.811 58.108 1627 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.87 % Allowed : 16.53 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1153 helix: 2.64 (0.43), residues: 134 sheet: -0.76 (0.24), residues: 452 loop : -1.99 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.004 0.001 HIS C 265 PHE 0.008 0.001 PHE C 243 TYR 0.013 0.001 TYR D 80 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 12) link_NAG-ASN : angle 3.09934 ( 36) link_BETA1-4 : bond 0.00662 ( 6) link_BETA1-4 : angle 1.97884 ( 18) hydrogen bonds : bond 0.04849 ( 295) hydrogen bonds : angle 4.80516 ( 822) SS BOND : bond 0.00286 ( 8) SS BOND : angle 1.11064 ( 16) covalent geometry : bond 0.00332 ( 9897) covalent geometry : angle 0.63100 (13494) ********************** 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 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.7401 (tt0) cc_final: 0.6974 (pt0) REVERT: D 30 ASP cc_start: 0.8489 (m-30) cc_final: 0.8149 (m-30) REVERT: C 269 ASP cc_start: 0.7784 (t0) cc_final: 0.7531 (t0) REVERT: B 381 ARG cc_start: 0.7541 (ttm110) cc_final: 0.7112 (mtp85) outliers start: 41 outliers final: 39 residues processed: 122 average time/residue: 0.2445 time to fit residues: 42.2623 Evaluate side-chains 127 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain B residue 144 LEU 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 232 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 HIS Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 431 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 51 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 0.0270 chunk 89 optimal weight: 6.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.177583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127393 restraints weight = 13524.003| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.36 r_work: 0.3522 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4033 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= 0.201 Angle : 0.696 13.509 13564 Z= 0.340 Chirality : 0.049 0.256 1563 Planarity : 0.005 0.054 1679 Dihedral : 7.816 59.376 1626 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.98 % Favored : 91.93 % Rotamer: Outliers : 4.06 % Allowed : 16.62 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1153 helix: 2.46 (0.42), residues: 134 sheet: -0.94 (0.23), residues: 461 loop : -1.92 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 457 HIS 0.006 0.001 HIS D 174 PHE 0.011 0.001 PHE B 328 TYR 0.018 0.002 TYR D 80 ARG 0.003 0.000 ARG C 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 12) link_NAG-ASN : angle 3.02278 ( 36) link_BETA1-4 : bond 0.00592 ( 6) link_BETA1-4 : angle 1.92898 ( 18) hydrogen bonds : bond 0.05452 ( 295) hydrogen bonds : angle 4.88468 ( 822) SS BOND : bond 0.00405 ( 8) SS BOND : angle 1.51626 ( 16) covalent geometry : bond 0.00482 ( 9897) covalent geometry : angle 0.67471 (13494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8469.21 seconds wall clock time: 149 minutes 39.63 seconds (8979.63 seconds total)