Starting phenix.real_space_refine on Thu Jul 2 08:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.map" model { file = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7b00_11952/07_2026/7b00_11952.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 27 5.16 5 C 4833 2.51 5 N 1179 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7389 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3542 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 25, 'TRANS': 431} Chain: "B" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 85 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.22, per 1000 atoms: 0.17 Number of scatterers: 7389 At special positions: 0 Unit cell: (81.6, 77.35, 129.2, 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 27 16.00 O 1350 8.00 N 1179 7.00 C 4833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS B 109 " 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN B 405 " " NAG D 1 " - " ASN B 264 " " NAG E 1 " - " ASN B 280 " " NAG F 1 " - " ASN B 323 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 257.8 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 48.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 4.818A pdb=" N ASN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.967A pdb=" N GLU A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 77 through 100 removed outlier: 4.190A pdb=" N GLY A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.851A pdb=" N LYS A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.643A pdb=" N GLY A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.761A pdb=" N SER A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.500A pdb=" N ILE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.510A pdb=" N ARG A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 186' Processing helix chain 'A' and resid 187 through 190 Processing helix chain 'A' and resid 191 through 212 removed outlier: 3.993A pdb=" N ILE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 4.498A pdb=" N VAL A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.728A pdb=" N VAL A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.870A pdb=" N THR A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.754A pdb=" N ALA A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.972A pdb=" N ALA A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.586A pdb=" N LEU A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 376 " --> pdb=" O CYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.828A pdb=" N ASN A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 removed outlier: 3.759A pdb=" N VAL A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 403 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 removed outlier: 3.808A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.699A pdb=" N LEU A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.738A pdb=" N TRP A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.288A pdb=" N MET A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 476 through 491 removed outlier: 3.688A pdb=" N ILE A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 73 removed outlier: 3.687A pdb=" N VAL B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 106 removed outlier: 3.535A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TRP B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 99 " --> pdb=" O MET B 95 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.534A pdb=" N HIS B 119 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 120 " --> pdb=" O TRP B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.729A pdb=" N GLN B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.898A pdb=" N LYS B 144 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 145 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.570A pdb=" N SER B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.503A pdb=" N THR B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 228' Processing helix chain 'B' and resid 228 through 239 removed outlier: 3.701A pdb=" N GLU B 234 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 removed outlier: 3.580A pdb=" N LEU B 252 " --> pdb=" O ILE B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.502A pdb=" N TRP B 262 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 3.716A pdb=" N ILE B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.993A pdb=" N THR B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 357 removed outlier: 3.520A pdb=" N GLN B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.565A pdb=" N MET B 406 " --> pdb=" O SER B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.918A pdb=" N ASP B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.596A pdb=" N HIS B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125 Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160 removed outlier: 6.277A pdb=" N LEU B 205 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ARG B 247 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 275 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 300 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA B 277 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.542A pdb=" N LYS B 165 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 442 removed outlier: 3.632A pdb=" N VAL B 465 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 519 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 520 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER B 497 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 522 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP B 493 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 508 " --> pdb=" O ALA B 492 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 627 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: 0.81 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2204 1.34 - 1.46: 1444 1.46 - 1.57: 3894 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 7583 Sorted by residual: bond pdb=" C56 AJP A 601 " pdb=" C57 AJP A 601 " ideal model delta sigma weight residual 1.522 1.558 -0.036 2.00e-02 2.50e+03 3.24e+00 bond pdb=" C65 AJP A 601 " pdb=" O64 AJP A 601 " ideal model delta sigma weight residual 1.373 1.408 -0.035 2.00e-02 2.50e+03 3.05e+00 bond pdb=" C57 AJP A 601 " pdb=" O64 AJP A 601 " ideal model delta sigma weight residual 1.414 1.443 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 7578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 9953 2.20 - 4.41: 321 4.41 - 6.61: 50 6.61 - 8.81: 23 8.81 - 11.01: 3 Bond angle restraints: 10350 Sorted by residual: angle pdb=" N ARG B 433 " pdb=" CA ARG B 433 " pdb=" C ARG B 433 " ideal model delta sigma weight residual 114.56 108.83 5.73 1.27e+00 6.20e-01 2.04e+01 angle pdb=" C PRO A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 120.33 123.54 -3.21 8.00e-01 1.56e+00 1.61e+01 angle pdb=" CA ILE A 365 " pdb=" C ILE A 365 " pdb=" N PRO A 366 " ideal model delta sigma weight residual 120.83 123.17 -2.34 6.10e-01 2.69e+00 1.47e+01 angle pdb=" C ASP A 230 " pdb=" N ILE A 231 " pdb=" CA ILE A 231 " ideal model delta sigma weight residual 121.97 128.74 -6.77 1.80e+00 3.09e-01 1.41e+01 angle pdb=" C SER A 444 " pdb=" N GLU A 445 " pdb=" CA GLU A 445 " ideal model delta sigma weight residual 121.80 130.57 -8.77 2.44e+00 1.68e-01 1.29e+01 ... (remaining 10345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 3712 16.06 - 32.12: 460 32.12 - 48.19: 129 48.19 - 64.25: 8 64.25 - 80.31: 6 Dihedral angle restraints: 4315 sinusoidal: 1667 harmonic: 2648 Sorted by residual: dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS B 109 " pdb=" CB CYS B 109 " ideal model delta sinusoidal sigma weight residual -86.00 -39.60 -46.40 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CA LEU A 350 " pdb=" C LEU A 350 " pdb=" N PRO A 351 " pdb=" CA PRO A 351 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA THR A 133 " pdb=" C THR A 133 " pdb=" N ASN A 134 " pdb=" CA ASN A 134 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 4312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 1231 0.331 - 0.662: 2 0.662 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.654: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 323 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.04e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.41e+01 ... (remaining 1231 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.343 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG F 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.069 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.272 2.00e-02 2.50e+03 2.27e-01 6.46e+02 pdb=" C7 NAG F 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.383 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.224 2.00e-02 2.50e+03 1.91e-01 4.55e+02 pdb=" C7 NAG D 2 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.313 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.173 2.00e-02 2.50e+03 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 32 2.45 - 3.06: 4159 3.06 - 3.68: 11042 3.68 - 4.29: 15290 4.29 - 4.90: 24995 Nonbonded interactions: 55518 Sorted by model distance: nonbonded pdb=" O3 NAG D 1 " pdb=" O6 NAG D 1 " model vdw 1.838 3.040 nonbonded pdb=" O ILE A 138 " pdb=" OG1 THR A 326 " model vdw 2.241 3.040 nonbonded pdb=" O GLY A 332 " pdb=" OG1 THR A 336 " model vdw 2.272 3.040 nonbonded pdb=" O SER B 305 " pdb=" OG SER B 305 " model vdw 2.286 3.040 nonbonded pdb=" O SER B 302 " pdb=" OG SER B 302 " model vdw 2.298 3.040 ... (remaining 55513 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.650 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.010 0.668 7593 Z= 0.809 Angle : 1.025 14.113 10376 Z= 0.506 Chirality : 0.076 1.654 1234 Planarity : 0.014 0.297 1265 Dihedral : 14.846 80.308 2616 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.39 % Allowed : 12.24 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.20 (0.17), residues: 922 helix: -4.76 (0.09), residues: 417 sheet: -1.62 (0.66), residues: 52 loop : -3.77 (0.21), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 122 TYR 0.022 0.002 TYR A 93 PHE 0.022 0.002 PHE A 226 TRP 0.018 0.002 TRP A 469 HIS 0.007 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.26 ( 7583) covalent geometry : angle 0.96811 / 0.49 (10350) SS BOND : bond 0.00107 / 0.07 ( 1) SS BOND : angle 1.40937 / 0.65 ( 2) hydrogen bonds : bond 0.34471 / 22.80 ( 215) hydrogen bonds : angle 11.56254 / 8.09 ( 627) Misc. bond : bond 0.66841 / 41.78 ( 1) link_BETA1-4 : bond 0.00098 / 0.07 ( 4) link_BETA1-4 : angle 0.31424 / 0.13 ( 12) link_NAG-ASN : bond 0.00527 / 0.33 ( 4) link_NAG-ASN : angle 9.94061 / 5.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8369 (pt) cc_final: 0.8114 (mm) REVERT: A 184 THR cc_start: 0.8874 (t) cc_final: 0.8473 (m) REVERT: A 211 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7678 (ttpp) REVERT: A 264 ASN cc_start: 0.7982 (m-40) cc_final: 0.7700 (m-40) REVERT: A 284 ASN cc_start: 0.8556 (m-40) cc_final: 0.7769 (t0) REVERT: B 146 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7238 (mmt90) REVERT: B 187 GLU cc_start: 0.7815 (pm20) cc_final: 0.7584 (pm20) REVERT: B 432 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7429 (tp30) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.0631 time to fit residues: 14.0766 Evaluate side-chains 121 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3796 r_free = 0.3796 target = 0.156065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122228 restraints weight = 10382.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121177 restraints weight = 15239.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122434 restraints weight = 15700.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122915 restraints weight = 10343.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123002 restraints weight = 10428.517| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7593 Z= 0.157 Angle : 0.764 12.552 10376 Z= 0.363 Chirality : 0.046 0.335 1234 Planarity : 0.005 0.046 1265 Dihedral : 5.892 28.712 992 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.58 % Allowed : 17.27 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.91 (0.21), residues: 922 helix: -3.36 (0.17), residues: 425 sheet: -1.80 (0.57), residues: 69 loop : -3.36 (0.25), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 338 TYR 0.013 0.001 TYR B 303 PHE 0.024 0.002 PHE A 155 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7583) covalent geometry : angle 0.72802 / 0.35 (10350) SS BOND : bond 0.00029 / 0.02 ( 1) SS BOND : angle 0.82948 / 0.36 ( 2) hydrogen bonds : bond 0.05899 / 3.99 ( 215) hydrogen bonds : angle 6.40454 / 4.61 ( 627) Misc. bond : bond 0.00139 / 0.09 ( 1) link_BETA1-4 : bond 0.00967 / 0.57 ( 4) link_BETA1-4 : angle 2.43919 / 1.29 ( 12) link_NAG-ASN : bond 0.00782 / 0.47 ( 4) link_NAG-ASN : angle 6.40727 / 3.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ASN cc_start: 0.8502 (m-40) cc_final: 0.7962 (t0) REVERT: A 314 MET cc_start: 0.5704 (tpt) cc_final: 0.5326 (tpt) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.0802 time to fit residues: 15.1568 Evaluate side-chains 124 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3785 r_free = 0.3785 target = 0.155066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121439 restraints weight = 10514.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120162 restraints weight = 17358.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121951 restraints weight = 15921.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121501 restraints weight = 11213.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122057 restraints weight = 10958.739| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7593 Z= 0.174 Angle : 0.726 11.854 10376 Z= 0.346 Chirality : 0.045 0.343 1234 Planarity : 0.004 0.046 1265 Dihedral : 5.624 31.478 992 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.77 % Allowed : 19.33 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.24), residues: 922 helix: -2.58 (0.21), residues: 438 sheet: -1.75 (0.58), residues: 69 loop : -3.13 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.012 0.001 TYR A 109 PHE 0.024 0.002 PHE A 155 TRP 0.009 0.001 TRP A 124 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 7583) covalent geometry : angle 0.69593 / 0.34 (10350) SS BOND : bond 0.00095 / 0.06 ( 1) SS BOND : angle 0.89391 / 0.39 ( 2) hydrogen bonds : bond 0.04742 / 3.18 ( 215) hydrogen bonds : angle 5.66523 / 4.06 ( 627) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : bond 0.00599 / 0.33 ( 4) link_BETA1-4 : angle 2.08266 / 1.11 ( 12) link_NAG-ASN : bond 0.00658 / 0.41 ( 4) link_NAG-ASN : angle 5.81477 / 2.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.0748 (OUTLIER) cc_final: 0.0539 (tt) REVERT: A 284 ASN cc_start: 0.8576 (m-40) cc_final: 0.8034 (t0) REVERT: A 471 HIS cc_start: 0.3777 (OUTLIER) cc_final: 0.2408 (m-70) REVERT: B 146 ARG cc_start: 0.7551 (mmt180) cc_final: 0.7312 (mmt180) REVERT: B 347 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6435 (pp30) outliers start: 37 outliers final: 25 residues processed: 146 average time/residue: 0.0738 time to fit residues: 15.1439 Evaluate side-chains 138 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 0.0570 chunk 0 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 518 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 = 0.3814 r_free = 0.3814 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122340 restraints weight = 10387.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121715 restraints weight = 13675.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123047 restraints weight = 16089.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123098 restraints weight = 10199.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123876 restraints weight = 10199.975| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7593 Z= 0.115 Angle : 0.683 11.337 10376 Z= 0.320 Chirality : 0.043 0.332 1234 Planarity : 0.004 0.044 1265 Dihedral : 5.189 32.118 992 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.38 % Allowed : 20.75 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.25), residues: 922 helix: -2.12 (0.22), residues: 437 sheet: -1.48 (0.60), residues: 70 loop : -2.97 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.013 0.001 TYR B 149 PHE 0.025 0.001 PHE A 155 TRP 0.038 0.001 TRP B 262 HIS 0.003 0.001 HIS A 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 7583) covalent geometry : angle 0.65443 / 0.31 (10350) SS BOND : bond 0.00130 / 0.08 ( 1) SS BOND : angle 0.45854 / 0.20 ( 2) hydrogen bonds : bond 0.03739 / 2.53 ( 215) hydrogen bonds : angle 5.25907 / 3.80 ( 627) Misc. bond : bond 0.00026 / 0.02 ( 1) link_BETA1-4 : bond 0.00762 / 0.42 ( 4) link_BETA1-4 : angle 2.17682 / 1.16 ( 12) link_NAG-ASN : bond 0.00657 / 0.41 ( 4) link_NAG-ASN : angle 5.36519 / 2.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8722 (mm) cc_final: 0.8277 (mt) REVERT: A 228 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.4620 (pm20) REVERT: A 284 ASN cc_start: 0.8491 (m-40) cc_final: 0.7969 (t0) REVERT: A 314 MET cc_start: 0.5904 (tpt) cc_final: 0.5690 (tpt) REVERT: A 471 HIS cc_start: 0.3744 (OUTLIER) cc_final: 0.2380 (m-70) REVERT: B 146 ARG cc_start: 0.7494 (mmt180) cc_final: 0.7280 (mmt180) REVERT: B 262 TRP cc_start: 0.8181 (m-90) cc_final: 0.7904 (m-90) REVERT: B 347 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6430 (pp30) outliers start: 34 outliers final: 23 residues processed: 144 average time/residue: 0.0711 time to fit residues: 14.9323 Evaluate side-chains 139 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3794 r_free = 0.3794 target = 0.156121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121596 restraints weight = 10450.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119411 restraints weight = 15622.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120660 restraints weight = 15060.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121203 restraints weight = 11021.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121055 restraints weight = 11414.816| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7593 Z= 0.150 Angle : 0.703 10.990 10376 Z= 0.327 Chirality : 0.045 0.336 1234 Planarity : 0.004 0.045 1265 Dihedral : 5.184 33.485 992 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.15 % Allowed : 21.01 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.26), residues: 922 helix: -1.90 (0.23), residues: 444 sheet: -1.41 (0.63), residues: 69 loop : -2.87 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.011 0.001 TYR B 149 PHE 0.033 0.002 PHE A 155 TRP 0.021 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7583) covalent geometry : angle 0.67663 / 0.32 (10350) SS BOND : bond 0.00060 / 0.04 ( 1) SS BOND : angle 0.72631 / 0.33 ( 2) hydrogen bonds : bond 0.03741 / 2.55 ( 215) hydrogen bonds : angle 5.21731 / 3.76 ( 627) Misc. bond : bond 0.00256 / 0.16 ( 1) link_BETA1-4 : bond 0.00659 / 0.36 ( 4) link_BETA1-4 : angle 2.06523 / 1.10 ( 12) link_NAG-ASN : bond 0.00599 / 0.37 ( 4) link_NAG-ASN : angle 5.26163 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8825 (mm) cc_final: 0.8321 (mt) REVERT: A 124 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7359 (t60) REVERT: A 228 GLU cc_start: 0.5427 (OUTLIER) cc_final: 0.4614 (pm20) REVERT: A 284 ASN cc_start: 0.8546 (m-40) cc_final: 0.7984 (t0) REVERT: A 314 MET cc_start: 0.6092 (tpt) cc_final: 0.5792 (tpt) REVERT: A 471 HIS cc_start: 0.3830 (OUTLIER) cc_final: 0.2473 (m-70) REVERT: B 146 ARG cc_start: 0.7558 (mmt180) cc_final: 0.7329 (mmt180) REVERT: B 347 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6515 (pp30) outliers start: 40 outliers final: 28 residues processed: 140 average time/residue: 0.0679 time to fit residues: 13.6574 Evaluate side-chains 139 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3814 r_free = 0.3814 target = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123621 restraints weight = 10324.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122482 restraints weight = 15791.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123897 restraints weight = 15495.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124314 restraints weight = 10692.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124460 restraints weight = 10899.293| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7593 Z= 0.120 Angle : 0.685 10.624 10376 Z= 0.315 Chirality : 0.044 0.331 1234 Planarity : 0.004 0.043 1265 Dihedral : 5.058 34.418 992 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.77 % Allowed : 21.91 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.26), residues: 922 helix: -1.71 (0.24), residues: 439 sheet: -1.34 (0.63), residues: 69 loop : -2.78 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 328 TYR 0.012 0.001 TYR B 303 PHE 0.030 0.001 PHE A 155 TRP 0.016 0.001 TRP B 262 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7583) covalent geometry : angle 0.66005 / 0.31 (10350) SS BOND : bond 0.00155 / 0.10 ( 1) SS BOND : angle 0.58176 / 0.28 ( 2) hydrogen bonds : bond 0.03433 / 2.31 ( 215) hydrogen bonds : angle 5.03274 / 3.64 ( 627) Misc. bond : bond 0.00245 / 0.15 ( 1) link_BETA1-4 : bond 0.00687 / 0.37 ( 4) link_BETA1-4 : angle 2.08248 / 1.11 ( 12) link_NAG-ASN : bond 0.00604 / 0.38 ( 4) link_NAG-ASN : angle 5.02257 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8780 (mm) cc_final: 0.8254 (mt) REVERT: A 124 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.7507 (t60) REVERT: A 184 THR cc_start: 0.8843 (t) cc_final: 0.8497 (m) REVERT: A 228 GLU cc_start: 0.5490 (OUTLIER) cc_final: 0.4672 (pm20) REVERT: A 284 ASN cc_start: 0.8512 (m-40) cc_final: 0.7970 (t0) REVERT: A 471 HIS cc_start: 0.3769 (OUTLIER) cc_final: 0.2438 (m-70) REVERT: B 146 ARG cc_start: 0.7529 (mmt180) cc_final: 0.7296 (mmt180) REVERT: B 262 TRP cc_start: 0.8286 (m-10) cc_final: 0.7962 (m-90) REVERT: B 347 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6489 (pp30) outliers start: 37 outliers final: 28 residues processed: 135 average time/residue: 0.0729 time to fit residues: 13.9352 Evaluate side-chains 138 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3805 r_free = 0.3805 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123149 restraints weight = 10438.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122613 restraints weight = 16015.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123925 restraints weight = 15471.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124578 restraints weight = 10245.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124926 restraints weight = 9937.047| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7593 Z= 0.137 Angle : 0.689 11.164 10376 Z= 0.319 Chirality : 0.045 0.332 1234 Planarity : 0.004 0.042 1265 Dihedral : 4.961 35.836 992 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.77 % Allowed : 22.42 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.26), residues: 922 helix: -1.52 (0.24), residues: 443 sheet: -1.40 (0.62), residues: 70 loop : -2.72 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.009 0.001 TYR B 149 PHE 0.027 0.002 PHE A 155 TRP 0.013 0.001 TRP B 262 HIS 0.003 0.001 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7583) covalent geometry : angle 0.66540 / 0.31 (10350) SS BOND : bond 0.00009 / 0.01 ( 1) SS BOND : angle 0.74635 / 0.36 ( 2) hydrogen bonds : bond 0.03379 / 2.29 ( 215) hydrogen bonds : angle 4.96169 / 3.57 ( 627) Misc. bond : bond 0.00188 / 0.12 ( 1) link_BETA1-4 : bond 0.00695 / 0.38 ( 4) link_BETA1-4 : angle 2.06986 / 1.11 ( 12) link_NAG-ASN : bond 0.00569 / 0.36 ( 4) link_NAG-ASN : angle 4.91211 / 2.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7613 (t60) REVERT: A 184 THR cc_start: 0.8876 (t) cc_final: 0.8510 (m) REVERT: A 228 GLU cc_start: 0.5373 (OUTLIER) cc_final: 0.4579 (pm20) REVERT: A 284 ASN cc_start: 0.8468 (m-40) cc_final: 0.8063 (t0) REVERT: A 460 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 464 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: A 471 HIS cc_start: 0.3758 (OUTLIER) cc_final: 0.2388 (m-70) REVERT: B 146 ARG cc_start: 0.7515 (mmt180) cc_final: 0.7297 (mmt180) REVERT: B 258 PHE cc_start: 0.6454 (m-80) cc_final: 0.6115 (m-80) REVERT: B 262 TRP cc_start: 0.8295 (m-10) cc_final: 0.7997 (m-90) REVERT: B 299 LEU cc_start: 0.8953 (tp) cc_final: 0.8745 (mt) REVERT: B 347 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6510 (pp30) outliers start: 37 outliers final: 28 residues processed: 136 average time/residue: 0.0769 time to fit residues: 14.8623 Evaluate side-chains 142 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.0010 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.0470 overall best weight: 0.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3839 r_free = 0.3839 target = 0.160812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126469 restraints weight = 10336.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124930 restraints weight = 15651.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126495 restraints weight = 15148.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126993 restraints weight = 10006.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.127421 restraints weight = 9949.869| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7593 Z= 0.100 Angle : 0.648 9.870 10376 Z= 0.298 Chirality : 0.042 0.324 1234 Planarity : 0.004 0.037 1265 Dihedral : 4.707 37.483 992 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.38 % Allowed : 23.07 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.27), residues: 922 helix: -1.26 (0.25), residues: 440 sheet: -1.21 (0.62), residues: 71 loop : -2.71 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.023 0.001 TYR B 303 PHE 0.027 0.001 PHE A 433 TRP 0.012 0.001 TRP B 262 HIS 0.002 0.001 HIS B 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7583) covalent geometry : angle 0.62543 / 0.29 (10350) SS BOND : bond 0.00225 / 0.14 ( 1) SS BOND : angle 0.62337 / 0.30 ( 2) hydrogen bonds : bond 0.02913 / 1.95 ( 215) hydrogen bonds : angle 4.64775 / 3.38 ( 627) Misc. bond : bond 0.00131 / 0.08 ( 1) link_BETA1-4 : bond 0.00701 / 0.38 ( 4) link_BETA1-4 : angle 2.13433 / 1.14 ( 12) link_NAG-ASN : bond 0.00631 / 0.40 ( 4) link_NAG-ASN : angle 4.60068 / 2.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6754 (mm) REVERT: A 184 THR cc_start: 0.8825 (t) cc_final: 0.8506 (m) REVERT: A 284 ASN cc_start: 0.8447 (m-40) cc_final: 0.8026 (t0) REVERT: A 460 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.7830 (p) REVERT: A 464 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5761 (m-10) REVERT: A 469 TRP cc_start: 0.4425 (p-90) cc_final: 0.3684 (p-90) REVERT: A 471 HIS cc_start: 0.3700 (OUTLIER) cc_final: 0.2398 (m-70) REVERT: B 146 ARG cc_start: 0.7442 (mmt180) cc_final: 0.7239 (mmt180) REVERT: B 262 TRP cc_start: 0.8294 (m-10) cc_final: 0.8004 (m-90) REVERT: B 347 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6545 (pp30) outliers start: 34 outliers final: 22 residues processed: 145 average time/residue: 0.0696 time to fit residues: 14.2843 Evaluate side-chains 142 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 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 = 0.3812 r_free = 0.3812 target = 0.158152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123828 restraints weight = 10286.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121545 restraints weight = 13360.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123245 restraints weight = 14562.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123485 restraints weight = 10072.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123729 restraints weight = 10938.069| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7593 Z= 0.143 Angle : 0.686 9.764 10376 Z= 0.319 Chirality : 0.045 0.329 1234 Planarity : 0.004 0.038 1265 Dihedral : 4.810 39.883 992 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.38 % Allowed : 23.20 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.27), residues: 922 helix: -1.17 (0.25), residues: 442 sheet: -1.29 (0.62), residues: 70 loop : -2.68 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 105 TYR 0.013 0.001 TYR A 109 PHE 0.036 0.002 PHE A 155 TRP 0.010 0.001 TRP B 262 HIS 0.003 0.001 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 7583) covalent geometry : angle 0.66456 / 0.31 (10350) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.86215 / 0.41 ( 2) hydrogen bonds : bond 0.03223 / 2.17 ( 215) hydrogen bonds : angle 4.77554 / 3.44 ( 627) Misc. bond : bond 0.00114 / 0.07 ( 1) link_BETA1-4 : bond 0.00647 / 0.35 ( 4) link_BETA1-4 : angle 2.05496 / 1.11 ( 12) link_NAG-ASN : bond 0.00520 / 0.33 ( 4) link_NAG-ASN : angle 4.65492 / 2.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6804 (mm) REVERT: A 184 THR cc_start: 0.8855 (t) cc_final: 0.8531 (m) REVERT: A 228 GLU cc_start: 0.5492 (OUTLIER) cc_final: 0.4556 (pm20) REVERT: A 284 ASN cc_start: 0.8418 (m-40) cc_final: 0.8016 (t0) REVERT: A 460 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.7871 (m) REVERT: A 464 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.5635 (m-10) REVERT: A 469 TRP cc_start: 0.4459 (p-90) cc_final: 0.3594 (p-90) REVERT: A 471 HIS cc_start: 0.3802 (OUTLIER) cc_final: 0.2487 (m-70) REVERT: B 146 ARG cc_start: 0.7566 (mmt180) cc_final: 0.7352 (mmt180) REVERT: B 258 PHE cc_start: 0.6579 (m-80) cc_final: 0.6157 (m-80) REVERT: B 262 TRP cc_start: 0.8387 (m-10) cc_final: 0.8115 (m-90) REVERT: B 347 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6512 (pp30) outliers start: 34 outliers final: 22 residues processed: 136 average time/residue: 0.0721 time to fit residues: 13.8899 Evaluate side-chains 137 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 82 optimal weight: 0.0030 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 54 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** B 518 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 = 0.3847 r_free = 0.3847 target = 0.161346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127299 restraints weight = 10228.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125770 restraints weight = 14850.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127073 restraints weight = 15278.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127903 restraints weight = 10221.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128040 restraints weight = 9832.739| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7593 Z= 0.107 Angle : 0.695 10.369 10376 Z= 0.317 Chirality : 0.044 0.325 1234 Planarity : 0.004 0.036 1265 Dihedral : 4.816 39.449 992 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.99 % Allowed : 24.36 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.27), residues: 922 helix: -1.00 (0.25), residues: 440 sheet: -1.13 (0.66), residues: 60 loop : -2.57 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.025 0.001 TYR B 303 PHE 0.038 0.001 PHE A 155 TRP 0.012 0.001 TRP B 117 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7583) covalent geometry : angle 0.67513 / 0.31 (10350) SS BOND : bond 0.00108 / 0.07 ( 1) SS BOND : angle 0.78267 / 0.35 ( 2) hydrogen bonds : bond 0.02951 / 2.00 ( 215) hydrogen bonds : angle 4.61496 / 3.37 ( 627) Misc. bond : bond 0.00581 / 0.36 ( 1) link_BETA1-4 : bond 0.00718 / 0.39 ( 4) link_BETA1-4 : angle 2.12455 / 1.14 ( 12) link_NAG-ASN : bond 0.00598 / 0.38 ( 4) link_NAG-ASN : angle 4.42027 / 2.19 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.8482 (mm) cc_final: 0.8101 (mt) REVERT: A 184 THR cc_start: 0.8818 (t) cc_final: 0.8544 (m) REVERT: A 228 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4565 (pm20) REVERT: A 284 ASN cc_start: 0.8439 (m-40) cc_final: 0.8048 (t0) REVERT: A 412 LYS cc_start: 0.6550 (mmtp) cc_final: 0.6323 (mttt) REVERT: A 460 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7832 (m) REVERT: A 469 TRP cc_start: 0.4357 (p-90) cc_final: 0.3647 (p-90) REVERT: A 471 HIS cc_start: 0.3660 (OUTLIER) cc_final: 0.2406 (m-70) REVERT: B 146 ARG cc_start: 0.7403 (mmt180) cc_final: 0.7202 (mmt180) REVERT: B 262 TRP cc_start: 0.8303 (m-10) cc_final: 0.8071 (m-90) REVERT: B 347 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6554 (pp30) outliers start: 31 outliers final: 24 residues processed: 141 average time/residue: 0.0714 time to fit residues: 13.9437 Evaluate side-chains 139 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 471 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 10 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 90 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 1 optimal weight: 0.2980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 518 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 = 0.3846 r_free = 0.3846 target = 0.161307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126745 restraints weight = 10277.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124051 restraints weight = 15896.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126063 restraints weight = 14471.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125825 restraints weight = 10108.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125991 restraints weight = 11314.712| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7593 Z= 0.113 Angle : 0.688 9.519 10376 Z= 0.318 Chirality : 0.045 0.327 1234 Planarity : 0.003 0.040 1265 Dihedral : 4.784 40.999 992 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.99 % Allowed : 25.13 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.27), residues: 922 helix: -0.89 (0.25), residues: 439 sheet: -1.07 (0.66), residues: 60 loop : -2.53 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 162 TYR 0.016 0.001 TYR A 109 PHE 0.036 0.002 PHE A 155 TRP 0.010 0.001 TRP B 262 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7583) covalent geometry : angle 0.66877 / 0.31 (10350) SS BOND : bond 0.00036 / 0.02 ( 1) SS BOND : angle 0.83149 / 0.39 ( 2) hydrogen bonds : bond 0.02986 / 2.01 ( 215) hydrogen bonds : angle 4.60289 / 3.36 ( 627) Misc. bond : bond 0.00581 / 0.36 ( 1) link_BETA1-4 : bond 0.00746 / 0.41 ( 4) link_BETA1-4 : angle 2.09892 / 1.13 ( 12) link_NAG-ASN : bond 0.00576 / 0.37 ( 4) link_NAG-ASN : angle 4.36907 / 2.16 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.21 seconds wall clock time: 21 minutes 1.96 seconds (1261.96 seconds total)