Starting phenix.real_space_refine on Fri Mar 14 07:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d7r_27231/03_2025/8d7r_27231.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d7r_27231/03_2025/8d7r_27231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2025/8d7r_27231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2025/8d7r_27231.map" model { file = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2025/8d7r_27231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d7r_27231/03_2025/8d7r_27231.cif" } resolution = 3.9 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= 0.018 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 36 5.16 5 C 6158 2.51 5 N 1608 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1432 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 16, 'TRANS': 161} 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: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3167 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 25, 'TRANS': 366} 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: "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 Chain: "B" 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 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.16, per 1000 atoms: 0.64 Number of scatterers: 9627 At special positions: 0 Unit cell: (102.34, 144.48, 151.36, 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 36 16.00 O 1825 8.00 N 1608 7.00 C 6158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 144 " distance=2.04 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 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-ASN " NAG A 701 " - " ASN A 131 " " NAG A 702 " - " ASN A 157 " " NAG A 703 " - " ASN A 383 " " NAG A 704 " - " ASN A 379 " " NAG B 901 " - " ASN B 426 " " NAG C 401 " - " ASN C 142 " " NAG E 1 " - " ASN C 190 " " NAG F 1 " - " ASN B 407 " " NAG G 1 " - " ASN B 303 " " NAG H 1 " - " ASN B 243 " " NAG I 1 " - " ASN A 227 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 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: 8 helices and 21 sheets defined 12.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'D' and resid 35 through 65 removed outlier: 3.987A pdb=" N SER D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 40 " --> pdb=" O PRO D 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 71 removed outlier: 3.699A pdb=" N ASN D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 66 through 71' Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.969A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 124 Processing helix chain 'D' and resid 126 through 154 Processing helix chain 'D' and resid 176 through 210 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 355 through 360 Processing sheet with id=AA1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AA2, first strand: chain 'C' and resid 211 through 214 Processing sheet with id=AA3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.875A pdb=" N ASN B 143 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 156 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 152 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 157 " --> pdb=" O HIS B 201 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS B 201 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.565A pdb=" N ASN B 191 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG B 221 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 175 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 219 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 177 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS B 216 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 244 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 242 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255 removed outlier: 3.720A pdb=" N ILE B 267 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 301 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 269 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 297 " --> pdb=" O CYS B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.652A pdb=" N ILE B 261 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 330 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 323 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 315 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 280 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR B 317 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 342 removed outlier: 5.712A pdb=" N GLN B 338 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN B 354 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 340 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 352 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 379 through 381 removed outlier: 3.844A pdb=" N VAL B 380 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 371 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 409 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR B 406 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 425 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 421 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 419 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 481 removed outlier: 3.688A pdb=" N ARG B 510 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 469 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 508 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS B 471 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 137 removed outlier: 7.684A pdb=" N VAL A 136 " --> pdb=" O LYS A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.613A pdb=" N LYS A 161 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 197 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 194 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 214 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 196 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 212 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.527A pdb=" N ASN A 227 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 245 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 229 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 243 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 231 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.781A pdb=" N MET A 302 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 258 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG A 300 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 260 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 298 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 262 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 296 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.905A pdb=" N VAL A 347 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 389 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 349 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 387 " --> pdb=" O LEU A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.748A pdb=" N GLN A 378 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP A 365 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 403 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 397 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 396 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AC2, first strand: chain 'A' and resid 459 through 460 removed outlier: 4.019A pdb=" N CYS A 491 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 503 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 469 through 474 removed outlier: 3.568A pdb=" N ASP A 469 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 471 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 455 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 452 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 499 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 454 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 492 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 512 " --> pdb=" O TYR A 492 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 585 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: 2.34 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3010 1.34 - 1.46: 2438 1.46 - 1.58: 4403 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 9899 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 9894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 13120 1.41 - 2.82: 318 2.82 - 4.23: 53 4.23 - 5.63: 10 5.63 - 7.04: 7 Bond angle restraints: 13508 Sorted by residual: angle pdb=" C PRO A 434 " pdb=" N LYS A 435 " pdb=" CA LYS A 435 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ALA B 448 " pdb=" N VAL B 449 " pdb=" CA VAL B 449 " ideal model delta sigma weight residual 120.49 125.19 -4.70 1.38e+00 5.25e-01 1.16e+01 angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " ideal model delta sigma weight residual 114.17 110.31 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" CA GLY A 361 " pdb=" C GLY A 361 " pdb=" N LYS A 362 " ideal model delta sigma weight residual 114.23 116.74 -2.51 8.80e-01 1.29e+00 8.14e+00 angle pdb=" C LEU B 194 " pdb=" N ASN B 195 " pdb=" CA ASN B 195 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.08e+00 ... (remaining 13503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 5767 21.88 - 43.76: 270 43.76 - 65.64: 57 65.64 - 87.52: 9 87.52 - 109.39: 26 Dihedral angle restraints: 6129 sinusoidal: 2682 harmonic: 3447 Sorted by residual: dihedral pdb=" CB CYS A 172 " pdb=" SG CYS A 172 " pdb=" SG CYS A 182 " pdb=" CB CYS A 182 " ideal model delta sinusoidal sigma weight residual 93.00 173.22 -80.22 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS A 458 " pdb=" SG CYS A 458 " pdb=" SG CYS A 466 " pdb=" CB CYS A 466 " ideal model delta sinusoidal sigma weight residual -86.00 -34.89 -51.11 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS C 116 " pdb=" SG CYS C 116 " pdb=" SG CYS C 127 " pdb=" CB CYS C 127 " ideal model delta sinusoidal sigma weight residual 93.00 60.67 32.33 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1270 0.049 - 0.098: 198 0.098 - 0.147: 76 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 190 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+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 -2.24 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 383 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1544 not shown) Planarity restraints: 1696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 66 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO D 67 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 500 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 501 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 273 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.022 5.00e-02 4.00e+02 ... (remaining 1693 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3184 2.86 - 3.37: 8390 3.37 - 3.88: 14623 3.88 - 4.39: 15262 4.39 - 4.90: 26904 Nonbonded interactions: 68363 Sorted by model distance: nonbonded pdb=" NH1 ARG A 262 " pdb=" O THR A 263 " model vdw 2.345 3.120 nonbonded pdb=" O GLU D 92 " pdb=" OG SER D 96 " model vdw 2.348 3.040 nonbonded pdb=" O TYR A 257 " pdb=" OG1 THR A 277 " model vdw 2.370 3.040 nonbonded pdb=" OG SER B 374 " pdb=" O5 NAG F 1 " model vdw 2.375 3.040 nonbonded pdb=" OE1 GLU B 373 " pdb=" N SER B 376 " model vdw 2.380 3.120 ... (remaining 68358 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 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 0.039 9899 Z= 0.173 Angle : 0.536 7.043 13508 Z= 0.271 Chirality : 0.042 0.245 1547 Planarity : 0.004 0.056 1685 Dihedral : 15.026 109.395 3865 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.21), residues: 1157 helix: 1.59 (0.42), residues: 129 sheet: -1.70 (0.28), residues: 305 loop : -3.30 (0.17), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 146 HIS 0.001 0.000 HIS A 340 PHE 0.013 0.000 PHE A 332 TYR 0.011 0.001 TYR B 502 ARG 0.001 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 MET cc_start: 0.5426 (ptp) cc_final: 0.4966 (mpp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2631 time to fit residues: 63.8773 Evaluate side-chains 99 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.0030 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS D 123 GLN D 135 HIS D 192 GLN C 162 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN C 256 HIS B 190 HIS B 201 HIS B 226 ASN B 286 ASN B 402 ASN B 420 GLN B 434 HIS B 454 HIS A 137 ASN A 287 GLN A 348 GLN A 471 GLN A 478 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.179658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.158336 restraints weight = 19019.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.157639 restraints weight = 24694.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.158249 restraints weight = 21712.610| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9899 Z= 0.365 Angle : 0.864 13.680 13508 Z= 0.422 Chirality : 0.054 0.404 1547 Planarity : 0.006 0.073 1685 Dihedral : 11.808 86.757 1592 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.46 % Allowed : 14.46 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.22), residues: 1157 helix: 1.59 (0.46), residues: 135 sheet: -1.90 (0.25), residues: 365 loop : -2.88 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 269 HIS 0.006 0.001 HIS B 344 PHE 0.041 0.003 PHE C 141 TYR 0.028 0.003 TYR D 49 ARG 0.005 0.001 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6058 (t0) REVERT: B 438 SER cc_start: 0.7293 (p) cc_final: 0.6996 (m) REVERT: A 213 ASN cc_start: 0.7895 (t0) cc_final: 0.7257 (p0) REVERT: A 351 TRP cc_start: 0.6521 (p90) cc_final: 0.5694 (p90) outliers start: 26 outliers final: 17 residues processed: 142 average time/residue: 0.2394 time to fit residues: 46.1903 Evaluate side-chains 117 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 478 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 100 optimal weight: 0.0370 chunk 82 optimal weight: 0.6980 chunk 106 optimal weight: 0.0020 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS A 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.182939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.159503 restraints weight = 19896.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.158720 restraints weight = 25740.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.160308 restraints weight = 19738.691| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9899 Z= 0.177 Angle : 0.655 11.197 13508 Z= 0.313 Chirality : 0.048 0.668 1547 Planarity : 0.004 0.042 1685 Dihedral : 9.742 80.770 1592 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.36 % Allowed : 16.26 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.23), residues: 1157 helix: 2.55 (0.48), residues: 135 sheet: -1.59 (0.26), residues: 363 loop : -2.64 (0.21), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 246 HIS 0.008 0.001 HIS A 478 PHE 0.010 0.001 PHE D 185 TYR 0.012 0.001 TYR A 322 ARG 0.007 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: C 245 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7295 (ptm160) REVERT: C 252 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5926 (t0) REVERT: A 313 TRP cc_start: 0.7168 (m100) cc_final: 0.6528 (m100) REVERT: A 328 LYS cc_start: 0.6446 (tmtt) cc_final: 0.6110 (tttm) REVERT: A 351 TRP cc_start: 0.5870 (p90) cc_final: 0.5570 (p90) outliers start: 25 outliers final: 13 residues processed: 128 average time/residue: 0.2451 time to fit residues: 43.6485 Evaluate side-chains 113 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 74 optimal weight: 0.0870 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN ** C 147 HIS ** 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 = 0.4511 r_free = 0.4511 target = 0.183159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.159462 restraints weight = 18975.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.159416 restraints weight = 22858.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.160737 restraints weight = 17308.110| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9899 Z= 0.169 Angle : 0.626 8.391 13508 Z= 0.300 Chirality : 0.046 0.560 1547 Planarity : 0.004 0.046 1685 Dihedral : 8.393 71.570 1592 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.27 % Allowed : 17.20 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.24), residues: 1157 helix: 2.80 (0.47), residues: 135 sheet: -1.33 (0.26), residues: 366 loop : -2.47 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 519 HIS 0.019 0.001 HIS A 478 PHE 0.009 0.001 PHE A 332 TYR 0.008 0.001 TYR A 295 ARG 0.008 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8783 (tt) cc_final: 0.8554 (tp) REVERT: C 245 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7266 (ptm160) REVERT: C 275 GLU cc_start: 0.5508 (mm-30) cc_final: 0.5184 (tm-30) REVERT: A 313 TRP cc_start: 0.7177 (m100) cc_final: 0.6547 (m100) REVERT: A 328 LYS cc_start: 0.6519 (tmtt) cc_final: 0.6207 (tttm) REVERT: A 351 TRP cc_start: 0.5916 (p90) cc_final: 0.5599 (p90) outliers start: 24 outliers final: 15 residues processed: 124 average time/residue: 0.2412 time to fit residues: 40.8216 Evaluate side-chains 116 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.181560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159541 restraints weight = 18982.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.158906 restraints weight = 26068.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.160169 restraints weight = 20177.365| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9899 Z= 0.175 Angle : 0.626 10.162 13508 Z= 0.301 Chirality : 0.045 0.447 1547 Planarity : 0.004 0.043 1685 Dihedral : 7.589 60.516 1592 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.55 % Allowed : 18.34 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1157 helix: 3.24 (0.46), residues: 129 sheet: -1.11 (0.27), residues: 360 loop : -2.33 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 443 HIS 0.012 0.001 HIS A 478 PHE 0.009 0.001 PHE D 185 TYR 0.024 0.001 TYR B 502 ARG 0.007 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LEU cc_start: 0.8806 (tt) cc_final: 0.8535 (tp) REVERT: C 245 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7171 (ptm160) REVERT: C 275 GLU cc_start: 0.5631 (mm-30) cc_final: 0.5368 (tm-30) REVERT: A 313 TRP cc_start: 0.7154 (m100) cc_final: 0.6642 (m100) REVERT: A 328 LYS cc_start: 0.6601 (tmtt) cc_final: 0.6297 (tttm) REVERT: A 351 TRP cc_start: 0.6048 (p90) cc_final: 0.5766 (p90) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.2365 time to fit residues: 41.8039 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.182515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.162523 restraints weight = 19280.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.161807 restraints weight = 24243.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.162286 restraints weight = 23113.531| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9899 Z= 0.157 Angle : 0.609 11.457 13508 Z= 0.293 Chirality : 0.043 0.301 1547 Planarity : 0.004 0.045 1685 Dihedral : 7.235 55.589 1592 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.46 % Allowed : 18.71 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.24), residues: 1157 helix: 3.38 (0.46), residues: 129 sheet: -0.97 (0.27), residues: 363 loop : -2.20 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 203 HIS 0.009 0.001 HIS A 478 PHE 0.007 0.001 PHE C 243 TYR 0.007 0.001 TYR A 295 ARG 0.011 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.6613 (mmt90) cc_final: 0.6356 (mmm160) REVERT: C 245 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7233 (ptm160) REVERT: A 206 LYS cc_start: 0.3884 (pptt) cc_final: 0.3087 (pptt) REVERT: A 313 TRP cc_start: 0.7154 (m100) cc_final: 0.6781 (m100) REVERT: A 328 LYS cc_start: 0.6606 (tmtt) cc_final: 0.6325 (tttm) outliers start: 26 outliers final: 17 residues processed: 132 average time/residue: 0.2367 time to fit residues: 42.9467 Evaluate side-chains 121 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.0020 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN C 298 HIS B 434 HIS A 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.175801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.153877 restraints weight = 19311.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.153035 restraints weight = 26179.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.153961 restraints weight = 23411.746| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9899 Z= 0.239 Angle : 0.689 12.341 13508 Z= 0.334 Chirality : 0.045 0.255 1547 Planarity : 0.005 0.043 1685 Dihedral : 7.075 57.084 1592 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.69 % Allowed : 18.43 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.24), residues: 1157 helix: 3.18 (0.46), residues: 129 sheet: -1.09 (0.26), residues: 372 loop : -2.20 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 351 HIS 0.007 0.001 HIS A 478 PHE 0.014 0.002 PHE D 185 TYR 0.021 0.002 TYR A 322 ARG 0.011 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.6682 (mmt90) cc_final: 0.6405 (mmm160) REVERT: C 245 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7549 (ptm160) REVERT: A 206 LYS cc_start: 0.4279 (pptt) cc_final: 0.3408 (pptt) REVERT: A 313 TRP cc_start: 0.7400 (m100) cc_final: 0.6978 (m100) REVERT: A 328 LYS cc_start: 0.6893 (tmtt) cc_final: 0.6603 (tttm) outliers start: 39 outliers final: 27 residues processed: 132 average time/residue: 0.2277 time to fit residues: 41.4447 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 75 ASN Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 HIS ** A 471 GLN ** 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 = 0.4429 r_free = 0.4429 target = 0.175900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.154576 restraints weight = 19290.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153688 restraints weight = 27614.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.154896 restraints weight = 22116.497| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9899 Z= 0.199 Angle : 0.665 13.471 13508 Z= 0.322 Chirality : 0.044 0.217 1547 Planarity : 0.004 0.047 1685 Dihedral : 6.896 59.808 1592 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.21 % Allowed : 19.38 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.24), residues: 1157 helix: 3.28 (0.45), residues: 129 sheet: -0.97 (0.27), residues: 368 loop : -2.25 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 351 HIS 0.014 0.001 HIS B 434 PHE 0.021 0.001 PHE A 332 TYR 0.018 0.001 TYR A 366 ARG 0.011 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8105 (mp) REVERT: C 245 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7309 (ptm160) REVERT: A 206 LYS cc_start: 0.4269 (pptt) cc_final: 0.3418 (pptt) REVERT: A 328 LYS cc_start: 0.7134 (tmtt) cc_final: 0.6893 (tttm) outliers start: 34 outliers final: 26 residues processed: 129 average time/residue: 0.2360 time to fit residues: 41.9698 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 5.9990 chunk 27 optimal weight: 0.0020 chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 chunk 80 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 HIS ** A 471 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.179268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157861 restraints weight = 18972.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157226 restraints weight = 25241.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.158765 restraints weight = 20886.550| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9899 Z= 0.170 Angle : 0.654 12.066 13508 Z= 0.317 Chirality : 0.043 0.221 1547 Planarity : 0.004 0.050 1685 Dihedral : 6.619 57.260 1592 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.55 % Allowed : 20.13 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1157 helix: 3.52 (0.45), residues: 129 sheet: -0.83 (0.27), residues: 361 loop : -2.13 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 351 HIS 0.006 0.001 HIS A 478 PHE 0.015 0.001 PHE A 332 TYR 0.018 0.001 TYR A 366 ARG 0.013 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6625 (mmm160) REVERT: D 113 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8023 (mp) REVERT: C 245 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: A 206 LYS cc_start: 0.4238 (pptt) cc_final: 0.3388 (pptt) REVERT: A 328 LYS cc_start: 0.7084 (tmtt) cc_final: 0.6842 (tttm) REVERT: A 348 GLN cc_start: 0.6818 (tp-100) cc_final: 0.6414 (tt0) outliers start: 27 outliers final: 21 residues processed: 129 average time/residue: 0.2326 time to fit residues: 42.0481 Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** 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 = 0.4414 r_free = 0.4414 target = 0.174671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.152979 restraints weight = 19129.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.152096 restraints weight = 26251.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.153042 restraints weight = 23167.453| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9899 Z= 0.214 Angle : 0.683 12.544 13508 Z= 0.336 Chirality : 0.044 0.219 1547 Planarity : 0.005 0.057 1685 Dihedral : 6.521 55.298 1592 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.17 % Allowed : 20.42 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.24), residues: 1157 helix: 3.39 (0.45), residues: 126 sheet: -0.99 (0.27), residues: 362 loop : -2.18 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 519 HIS 0.006 0.001 HIS A 478 PHE 0.012 0.001 PHE A 332 TYR 0.023 0.001 TYR D 110 ARG 0.013 0.001 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.6929 (mmm160) cc_final: 0.6663 (mmm160) REVERT: D 154 LEU cc_start: 0.8653 (mm) cc_final: 0.8397 (mp) REVERT: C 245 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7511 (ptm160) REVERT: B 474 ASN cc_start: 0.6198 (t0) cc_final: 0.5739 (t0) REVERT: A 206 LYS cc_start: 0.4587 (pptt) cc_final: 0.3656 (pptt) REVERT: A 348 GLN cc_start: 0.7018 (tp-100) cc_final: 0.6693 (tt0) REVERT: A 414 LEU cc_start: 0.6808 (tt) cc_final: 0.6525 (tp) outliers start: 23 outliers final: 20 residues processed: 121 average time/residue: 0.2332 time to fit residues: 39.2202 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 HIS ** 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 = 0.4442 r_free = 0.4442 target = 0.176913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.155708 restraints weight = 19274.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.155081 restraints weight = 25395.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.156102 restraints weight = 21556.172| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9899 Z= 0.173 Angle : 0.651 11.380 13508 Z= 0.317 Chirality : 0.044 0.221 1547 Planarity : 0.004 0.054 1685 Dihedral : 6.379 55.620 1592 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.27 % Allowed : 20.23 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.24), residues: 1157 helix: 3.50 (0.45), residues: 126 sheet: -0.92 (0.28), residues: 359 loop : -2.08 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 519 HIS 0.005 0.001 HIS A 478 PHE 0.010 0.001 PHE C 125 TYR 0.014 0.001 TYR A 366 ARG 0.014 0.001 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.20 seconds wall clock time: 55 minutes 5.71 seconds (3305.71 seconds total)