Starting phenix.real_space_refine on Fri Sep 11 01:12:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dzv_8940/09_2026/6dzv_8940.cif" } resolution = 4.2 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= 0.003 sd= 0.522 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 34 5.16 5 C 4039 2.51 5 N 962 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6121 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} 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: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'HJM': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.62, per 1000 atoms: 0.26 Number of scatterers: 6121 At special positions: 0 Unit cell: (83.123, 76.539, 117.689, 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 34 16.00 O 1086 8.00 N 962 7.00 C 4039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 406.6 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 56.1% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.601A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.724A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.810A pdb=" N TYR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.826A pdb=" N LEU A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 128 through 144 removed outlier: 4.360A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.103A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 159 removed outlier: 3.550A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 160 through 190 removed outlier: 3.720A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 252 through 273 removed outlier: 3.667A pdb=" N ALA A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.588A pdb=" N VAL A 280 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.574A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.846A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 310 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 4.169A pdb=" N LYS A 319 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.785A pdb=" N ALA A 330 " --> pdb=" O TRP A 326 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 356 through 391 removed outlier: 3.525A pdb=" N ASP A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 373 " --> pdb=" O CYS A 369 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 389 " --> pdb=" O TYR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 4.074A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 414 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 454 removed outlier: 3.661A pdb=" N ILE A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 removed outlier: 4.254A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.717A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 4.569A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.507A pdb=" N ALA A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 removed outlier: 3.809A pdb=" N ARG A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 4.132A pdb=" N CYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 536 through 541' Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.806A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.575A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.717A pdb=" N ILE A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.702A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.882A pdb=" N GLU B 29 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 113 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 114 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 56 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP B 55 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 68 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 39 removed outlier: 3.662A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 97 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 92 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AA4, first strand: chain 'C' and resid 30 through 32 removed outlier: 5.852A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.314A pdb=" N ASN C 51 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 7.290A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN C 58 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 90 removed outlier: 3.661A pdb=" N SER C 89 " --> pdb=" O SER C 96 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 618 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: 0.94 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.16: 1 1.16 - 1.33: 955 1.33 - 1.49: 2754 1.49 - 1.65: 2541 1.65 - 1.81: 56 Bond restraints: 6307 Sorted by residual: bond pdb=" CBD Y01 A 704 " pdb=" CBG Y01 A 704 " ideal model delta sigma weight residual 1.520 1.001 0.519 2.00e-02 2.50e+03 6.73e+02 bond pdb=" CAS Y01 A 704 " pdb=" CAU Y01 A 704 " ideal model delta sigma weight residual 1.530 1.191 0.339 2.00e-02 2.50e+03 2.88e+02 bond pdb=" CAU Y01 A 704 " pdb=" CBI Y01 A 704 " ideal model delta sigma weight residual 1.530 1.254 0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" CAP Y01 A 704 " pdb=" CAQ Y01 A 704 " ideal model delta sigma weight residual 1.541 1.803 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" CAK Y01 A 704 " pdb=" CBD Y01 A 704 " ideal model delta sigma weight residual 1.525 1.264 0.261 2.00e-02 2.50e+03 1.70e+02 ... (remaining 6302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 8482 2.35 - 4.70: 81 4.70 - 7.05: 22 7.05 - 9.40: 9 9.40 - 11.75: 2 Bond angle restraints: 8596 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 133.45 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" CAK Y01 A 704 " pdb=" CAI Y01 A 704 " pdb=" CAZ Y01 A 704 " ideal model delta sigma weight residual 124.96 113.98 10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.51 119.43 -3.92 1.27e+00 6.20e-01 9.51e+00 angle pdb=" CAM Y01 A 704 " pdb=" CAY Y01 A 704 " pdb=" OAW Y01 A 704 " ideal model delta sigma weight residual 111.19 120.17 -8.98 3.00e+00 1.11e-01 8.96e+00 angle pdb=" CAQ Y01 A 704 " pdb=" CBG Y01 A 704 " pdb=" CBD Y01 A 704 " ideal model delta sigma weight residual 118.56 127.14 -8.58 3.00e+00 1.11e-01 8.18e+00 ... (remaining 8591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 3487 15.05 - 30.09: 77 30.09 - 45.14: 27 45.14 - 60.18: 3 60.18 - 75.23: 3 Dihedral angle restraints: 3597 sinusoidal: 1397 harmonic: 2200 Sorted by residual: dihedral pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta harmonic sigma weight residual 0.00 27.72 -27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CB MET A 124 " pdb=" CG MET A 124 " pdb=" SD MET A 124 " pdb=" CE MET A 124 " ideal model delta sinusoidal sigma weight residual 60.00 102.14 -42.14 3 1.50e+01 4.44e-03 7.56e+00 dihedral pdb=" CB MET A 260 " pdb=" CG MET A 260 " pdb=" SD MET A 260 " pdb=" CE MET A 260 " ideal model delta sinusoidal sigma weight residual 60.00 101.75 -41.75 3 1.50e+01 4.44e-03 7.48e+00 ... (remaining 3594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 949 0.317 - 0.633: 1 0.633 - 0.950: 2 0.950 - 1.267: 0 1.267 - 1.584: 1 Chirality restraints: 953 Sorted by residual: chirality pdb=" CBD Y01 A 704 " pdb=" CAK Y01 A 704 " pdb=" CBF Y01 A 704 " pdb=" CBG Y01 A 704 " both_signs ideal model delta sigma weight residual False 2.70 1.11 1.58 2.00e-01 2.50e+01 6.27e+01 chirality pdb=" CBG Y01 A 704 " pdb=" CAQ Y01 A 704 " pdb=" CBD Y01 A 704 " pdb=" CBI Y01 A 704 " both_signs ideal model delta sigma weight residual False -2.33 -1.63 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CBI Y01 A 704 " pdb=" CAU Y01 A 704 " pdb=" CBE Y01 A 704 " pdb=" CBG Y01 A 704 " both_signs ideal model delta sigma weight residual False 2.94 2.27 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 950 not shown) Planarity restraints: 1051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O HJM A 703 " -0.163 2.00e-02 2.50e+03 1.03e-01 3.16e+02 pdb=" C11 HJM A 703 " 0.031 2.00e-02 2.50e+03 pdb=" C12 HJM A 703 " 0.149 2.00e-02 2.50e+03 pdb=" C13 HJM A 703 " 0.070 2.00e-02 2.50e+03 pdb=" C15 HJM A 703 " 0.075 2.00e-02 2.50e+03 pdb=" C16 HJM A 703 " -0.004 2.00e-02 2.50e+03 pdb=" C17 HJM A 703 " 0.065 2.00e-02 2.50e+03 pdb=" C18 HJM A 703 " -0.011 2.00e-02 2.50e+03 pdb=" C19 HJM A 703 " -0.004 2.00e-02 2.50e+03 pdb=" C2 HJM A 703 " -0.229 2.00e-02 2.50e+03 pdb=" C8 HJM A 703 " -0.057 2.00e-02 2.50e+03 pdb=" N2 HJM A 703 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 417 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO A 418 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 155 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 156 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.019 5.00e-02 4.00e+02 ... (remaining 1048 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 66 2.65 - 3.21: 5806 3.21 - 3.78: 8553 3.78 - 4.34: 12529 4.34 - 4.90: 19883 Nonbonded interactions: 46837 Sorted by model distance: nonbonded pdb=" O ASN A 145 " pdb=" OG SER A 149 " model vdw 2.088 3.040 nonbonded pdb=" O MET A 260 " pdb=" OG1 THR A 264 " model vdw 2.090 3.040 nonbonded pdb=" O SER B 49 " pdb=" OH TYR B 71 " model vdw 2.119 3.040 nonbonded pdb=" OG1 THR A 221 " pdb=" OG SER A 224 " model vdw 2.121 3.040 nonbonded pdb=" O LEU A 478 " pdb=" OG1 THR A 482 " model vdw 2.140 3.040 ... (remaining 46832 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 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 : 0.013 0.519 6312 Z= 0.634 Angle : 0.709 11.748 8608 Z= 0.335 Chirality : 0.075 1.584 953 Planarity : 0.005 0.103 1050 Dihedral : 8.196 75.228 2192 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -4.08 (0.25), residues: 759 helix: -3.53 (0.16), residues: 283 sheet: -3.51 (0.51), residues: 73 loop : -1.83 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 144 TYR 0.007 0.001 TYR A 134 PHE 0.009 0.001 PHE A 474 TRP 0.008 0.001 TRP A 537 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.01273 / 0.63 ( 6307) covalent geometry : angle 0.70457 / 0.33 ( 8596) SS BOND : bond 0.00205 / 0.10 ( 3) SS BOND : angle 0.56803 / 0.29 ( 6) hydrogen bonds : bond 0.33104 / 22.22 ( 222) hydrogen bonds : angle 9.76081 / 6.97 ( 618) link_BETA1-4 : bond 0.00217 / 0.11 ( 1) link_BETA1-4 : angle 3.70605 / 2.01 ( 3) link_NAG-ASN : bond 0.01958 / 1.03 ( 1) link_NAG-ASN : angle 2.62600 / 1.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8800 (t80) cc_final: 0.8580 (t80) REVERT: A 157 ILE cc_start: 0.8426 (tt) cc_final: 0.8217 (mt) REVERT: A 186 TYR cc_start: 0.6988 (m-10) cc_final: 0.6758 (m-10) REVERT: A 253 TRP cc_start: 0.8190 (p-90) cc_final: 0.6784 (m100) REVERT: A 260 MET cc_start: 0.7397 (mmp) cc_final: 0.6648 (ttt) REVERT: A 332 GLN cc_start: 0.7369 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 414 ILE cc_start: 0.6104 (mm) cc_final: 0.5796 (mt) REVERT: A 495 TYR cc_start: 0.6069 (m-80) cc_final: 0.5795 (m-80) REVERT: A 558 MET cc_start: 0.8408 (mtm) cc_final: 0.8103 (tpt) REVERT: A 595 TYR cc_start: 0.7234 (m-10) cc_final: 0.6888 (m-80) REVERT: A 605 LYS cc_start: 0.8264 (tttt) cc_final: 0.7654 (pttt) REVERT: B 42 LYS cc_start: 0.8891 (tptt) cc_final: 0.8023 (tppt) REVERT: B 47 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7840 (ttp-110) REVERT: B 83 PHE cc_start: 0.7752 (m-80) cc_final: 0.7186 (m-10) REVERT: B 101 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8038 (tp40) REVERT: B 120 TYR cc_start: 0.5376 (m-80) cc_final: 0.4344 (m-80) REVERT: C 71 LEU cc_start: 0.8342 (mt) cc_final: 0.8064 (mm) REVERT: C 78 GLN cc_start: 0.7165 (mt0) cc_final: 0.6911 (mm-40) REVERT: C 118 VAL cc_start: 0.8148 (t) cc_final: 0.7820 (p) REVERT: C 130 ILE cc_start: 0.8802 (mt) cc_final: 0.8399 (mt) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.0943 time to fit residues: 34.6860 Evaluate side-chains 150 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.146482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.126578 restraints weight = 19448.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.130220 restraints weight = 12718.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.132809 restraints weight = 9100.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.134667 restraints weight = 6956.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.136077 restraints weight = 5591.350| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6312 Z= 0.179 Angle : 0.670 9.692 8608 Z= 0.346 Chirality : 0.047 0.318 953 Planarity : 0.005 0.035 1050 Dihedral : 5.767 59.468 882 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.16 % Allowed : 1.09 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -2.64 (0.28), residues: 759 helix: -1.34 (0.26), residues: 322 sheet: -2.65 (0.54), residues: 69 loop : -1.88 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 564 TYR 0.014 0.002 TYR A 410 PHE 0.036 0.002 PHE A 287 TRP 0.019 0.002 TRP C 120 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 ( 6307) covalent geometry : angle 0.66790 / 0.35 ( 8596) SS BOND : bond 0.00270 / 0.14 ( 3) SS BOND : angle 0.92819 / 0.52 ( 6) hydrogen bonds : bond 0.06676 / 4.28 ( 222) hydrogen bonds : angle 6.26563 / 4.63 ( 618) link_BETA1-4 : bond 0.00573 / 0.30 ( 1) link_BETA1-4 : angle 2.85597 / 1.60 ( 3) link_NAG-ASN : bond 0.00398 / 0.21 ( 1) link_NAG-ASN : angle 1.28600 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8957 (m-30) cc_final: 0.8594 (m-30) REVERT: A 142 TYR cc_start: 0.7639 (t80) cc_final: 0.7385 (t80) REVERT: A 158 PHE cc_start: 0.8571 (m-80) cc_final: 0.7970 (m-80) REVERT: A 260 MET cc_start: 0.7488 (mmp) cc_final: 0.6735 (ttt) REVERT: A 262 ILE cc_start: 0.8474 (mm) cc_final: 0.8215 (mm) REVERT: A 332 GLN cc_start: 0.7624 (tm-30) cc_final: 0.6823 (tm-30) REVERT: A 336 SER cc_start: 0.8779 (t) cc_final: 0.8556 (p) REVERT: A 414 ILE cc_start: 0.6617 (mm) cc_final: 0.6308 (mm) REVERT: A 454 PHE cc_start: 0.8604 (m-10) cc_final: 0.8315 (m-10) REVERT: A 461 ARG cc_start: 0.8857 (mtt90) cc_final: 0.8270 (mtt180) REVERT: A 471 ILE cc_start: 0.8650 (mt) cc_final: 0.8439 (mt) REVERT: A 547 LEU cc_start: 0.8642 (tp) cc_final: 0.8397 (tp) REVERT: A 558 MET cc_start: 0.8495 (mtm) cc_final: 0.8293 (tpt) REVERT: A 595 TYR cc_start: 0.7246 (m-10) cc_final: 0.6869 (m-80) REVERT: A 605 LYS cc_start: 0.8474 (tttt) cc_final: 0.8246 (tttm) REVERT: B 42 LYS cc_start: 0.8952 (tptt) cc_final: 0.8440 (tppt) REVERT: B 59 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7310 (ttt180) REVERT: B 83 PHE cc_start: 0.7636 (m-80) cc_final: 0.7375 (m-10) REVERT: B 88 THR cc_start: 0.8050 (p) cc_final: 0.7242 (p) REVERT: B 114 PHE cc_start: 0.7612 (m-80) cc_final: 0.7224 (m-80) REVERT: B 120 TYR cc_start: 0.6231 (m-80) cc_final: 0.5708 (m-10) REVERT: B 130 TRP cc_start: 0.8110 (m100) cc_final: 0.7574 (m100) REVERT: C 105 ASP cc_start: 0.8344 (m-30) cc_final: 0.8057 (m-30) REVERT: C 127 LYS cc_start: 0.8423 (mppt) cc_final: 0.8114 (mmtm) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0768 time to fit residues: 19.9559 Evaluate side-chains 147 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 177 ASN A 205 ASN A 254 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.141887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.122616 restraints weight = 20171.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.126094 restraints weight = 13337.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.128532 restraints weight = 9630.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.130326 restraints weight = 7447.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.131726 restraints weight = 5973.735| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6312 Z= 0.152 Angle : 0.608 9.446 8608 Z= 0.313 Chirality : 0.045 0.294 953 Planarity : 0.005 0.039 1050 Dihedral : 5.726 59.942 882 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.30), residues: 759 helix: -0.50 (0.27), residues: 332 sheet: -2.02 (0.53), residues: 81 loop : -1.68 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 462 TYR 0.020 0.001 TYR A 410 PHE 0.032 0.002 PHE A 287 TRP 0.017 0.001 TRP A 253 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6307) covalent geometry : angle 0.60566 / 0.31 ( 8596) SS BOND : bond 0.00408 / 0.20 ( 3) SS BOND : angle 0.94654 / 0.45 ( 6) hydrogen bonds : bond 0.04897 / 3.16 ( 222) hydrogen bonds : angle 5.48389 / 4.12 ( 618) link_BETA1-4 : bond 0.00284 / 0.15 ( 1) link_BETA1-4 : angle 2.57108 / 1.47 ( 3) link_NAG-ASN : bond 0.00367 / 0.19 ( 1) link_NAG-ASN : angle 1.26259 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8854 (m-30) cc_final: 0.8356 (m-30) REVERT: A 126 ILE cc_start: 0.6720 (tp) cc_final: 0.6502 (tp) REVERT: A 158 PHE cc_start: 0.8692 (m-80) cc_final: 0.8122 (m-80) REVERT: A 260 MET cc_start: 0.7345 (mmp) cc_final: 0.6508 (ttp) REVERT: A 290 ILE cc_start: 0.8422 (mm) cc_final: 0.8120 (mt) REVERT: A 332 GLN cc_start: 0.7684 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 461 ARG cc_start: 0.8839 (mtt90) cc_final: 0.8376 (mtt180) REVERT: A 547 LEU cc_start: 0.8675 (tp) cc_final: 0.8449 (tp) REVERT: A 595 TYR cc_start: 0.7120 (m-10) cc_final: 0.6729 (m-80) REVERT: A 605 LYS cc_start: 0.8502 (tttt) cc_final: 0.8244 (tttm) REVERT: A 606 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8881 (mm-30) REVERT: B 59 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7870 (ttt180) REVERT: B 70 ILE cc_start: 0.9457 (tt) cc_final: 0.9253 (mm) REVERT: B 88 THR cc_start: 0.8135 (p) cc_final: 0.7572 (p) REVERT: B 120 TYR cc_start: 0.6428 (m-80) cc_final: 0.5910 (m-80) REVERT: B 127 MET cc_start: 0.8866 (mmp) cc_final: 0.8474 (mmp) REVERT: C 31 LEU cc_start: 0.5304 (mm) cc_final: 0.4413 (mm) REVERT: C 54 ILE cc_start: 0.8682 (mm) cc_final: 0.8436 (tp) REVERT: C 105 ASP cc_start: 0.8365 (m-30) cc_final: 0.8093 (m-30) REVERT: C 127 LYS cc_start: 0.8592 (mppt) cc_final: 0.7925 (mppt) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.0838 time to fit residues: 20.7014 Evaluate side-chains 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 0.0010 chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.140586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121643 restraints weight = 20613.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.124978 restraints weight = 13856.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.127363 restraints weight = 10070.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.129148 restraints weight = 7754.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.130440 restraints weight = 6223.355| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6312 Z= 0.129 Angle : 0.595 9.500 8608 Z= 0.301 Chirality : 0.044 0.294 953 Planarity : 0.005 0.054 1050 Dihedral : 5.620 57.773 882 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.30), residues: 759 helix: 0.08 (0.28), residues: 328 sheet: -1.66 (0.57), residues: 75 loop : -1.50 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 462 TYR 0.018 0.001 TYR A 410 PHE 0.025 0.002 PHE A 423 TRP 0.018 0.001 TRP B 55 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6307) covalent geometry : angle 0.59224 / 0.30 ( 8596) SS BOND : bond 0.00221 / 0.11 ( 3) SS BOND : angle 1.12025 / 0.53 ( 6) hydrogen bonds : bond 0.04127 / 2.73 ( 222) hydrogen bonds : angle 5.17360 / 3.91 ( 618) link_BETA1-4 : bond 0.00355 / 0.19 ( 1) link_BETA1-4 : angle 2.27686 / 1.30 ( 3) link_NAG-ASN : bond 0.00373 / 0.20 ( 1) link_NAG-ASN : angle 1.22545 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8794 (m-30) cc_final: 0.8369 (m-30) REVERT: A 112 ASN cc_start: 0.8899 (m110) cc_final: 0.8545 (m110) REVERT: A 158 PHE cc_start: 0.8646 (m-80) cc_final: 0.8145 (m-80) REVERT: A 260 MET cc_start: 0.7332 (mmp) cc_final: 0.6542 (ttp) REVERT: A 290 ILE cc_start: 0.8490 (mm) cc_final: 0.8207 (mt) REVERT: A 332 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 461 ARG cc_start: 0.8858 (mtt90) cc_final: 0.8302 (mtt180) REVERT: A 544 ILE cc_start: 0.8314 (mm) cc_final: 0.7029 (mm) REVERT: A 547 LEU cc_start: 0.8618 (tp) cc_final: 0.8394 (tp) REVERT: A 595 TYR cc_start: 0.7085 (m-10) cc_final: 0.6647 (m-80) REVERT: A 605 LYS cc_start: 0.8435 (tttt) cc_final: 0.8169 (tttm) REVERT: B 42 LYS cc_start: 0.8967 (tptt) cc_final: 0.8468 (tppt) REVERT: B 59 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7633 (ttm170) REVERT: B 83 PHE cc_start: 0.7941 (m-80) cc_final: 0.7292 (m-10) REVERT: B 88 THR cc_start: 0.7893 (p) cc_final: 0.7556 (p) REVERT: B 120 TYR cc_start: 0.6544 (m-80) cc_final: 0.6042 (m-80) REVERT: C 54 ILE cc_start: 0.8703 (mm) cc_final: 0.8450 (tp) REVERT: C 105 ASP cc_start: 0.8379 (m-30) cc_final: 0.7854 (m-30) REVERT: C 127 LYS cc_start: 0.8152 (mppt) cc_final: 0.7759 (mppt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0766 time to fit residues: 18.9602 Evaluate side-chains 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.130221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.112434 restraints weight = 21772.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.115576 restraints weight = 14395.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117810 restraints weight = 10408.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.119453 restraints weight = 7972.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.120646 restraints weight = 6399.176| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.6709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 6312 Z= 0.207 Angle : 0.710 9.601 8608 Z= 0.364 Chirality : 0.046 0.288 953 Planarity : 0.005 0.059 1050 Dihedral : 6.279 58.380 882 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.30), residues: 759 helix: 0.11 (0.28), residues: 310 sheet: -1.39 (0.59), residues: 75 loop : -1.61 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 464 TYR 0.026 0.002 TYR A 410 PHE 0.019 0.002 PHE A 380 TRP 0.019 0.002 TRP A 253 HIS 0.003 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 ( 6307) covalent geometry : angle 0.70765 / 0.36 ( 8596) SS BOND : bond 0.00762 / 0.38 ( 3) SS BOND : angle 1.65188 / 0.86 ( 6) hydrogen bonds : bond 0.04174 / 2.77 ( 222) hydrogen bonds : angle 5.42121 / 4.09 ( 618) link_BETA1-4 : bond 0.00005 / 0.00 ( 1) link_BETA1-4 : angle 2.47114 / 1.40 ( 3) link_NAG-ASN : bond 0.00359 / 0.19 ( 1) link_NAG-ASN : angle 0.80544 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.9105 (m110) cc_final: 0.8858 (m110) REVERT: A 158 PHE cc_start: 0.8766 (m-80) cc_final: 0.8291 (m-10) REVERT: A 260 MET cc_start: 0.7386 (mmp) cc_final: 0.6739 (ttp) REVERT: A 392 GLU cc_start: 0.8439 (tp30) cc_final: 0.7898 (tp30) REVERT: A 396 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7834 (mp0) REVERT: A 461 ARG cc_start: 0.8885 (mtt90) cc_final: 0.8294 (mtt180) REVERT: A 527 GLU cc_start: 0.8917 (mp0) cc_final: 0.8549 (pm20) REVERT: A 595 TYR cc_start: 0.7295 (m-10) cc_final: 0.6660 (m-80) REVERT: A 606 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8946 (mm-30) REVERT: B 42 LYS cc_start: 0.8871 (tptt) cc_final: 0.8427 (tppt) REVERT: B 59 ARG cc_start: 0.8343 (ttt180) cc_final: 0.8086 (ttt180) REVERT: B 88 THR cc_start: 0.7873 (p) cc_final: 0.7508 (p) REVERT: B 120 TYR cc_start: 0.6704 (m-80) cc_final: 0.6189 (m-80) REVERT: B 127 MET cc_start: 0.8989 (mmp) cc_final: 0.8717 (mmp) REVERT: C 54 ILE cc_start: 0.8751 (mm) cc_final: 0.8497 (tp) REVERT: C 105 ASP cc_start: 0.8094 (m-30) cc_final: 0.7883 (m-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0806 time to fit residues: 18.4659 Evaluate side-chains 142 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.134644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116529 restraints weight = 20043.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.119846 restraints weight = 12735.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.122156 restraints weight = 9051.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.123854 restraints weight = 6907.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.125152 restraints weight = 5491.397| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6312 Z= 0.125 Angle : 0.618 9.644 8608 Z= 0.317 Chirality : 0.044 0.284 953 Planarity : 0.005 0.037 1050 Dihedral : 5.951 58.645 882 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.92 (0.30), residues: 759 helix: 0.40 (0.28), residues: 322 sheet: -1.19 (0.59), residues: 75 loop : -1.40 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.020 0.001 TYR A 410 PHE 0.015 0.001 PHE A 133 TRP 0.021 0.001 TRP A 253 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6307) covalent geometry : angle 0.61592 / 0.32 ( 8596) SS BOND : bond 0.00315 / 0.16 ( 3) SS BOND : angle 1.11118 / 0.55 ( 6) hydrogen bonds : bond 0.03873 / 2.56 ( 222) hydrogen bonds : angle 5.07678 / 3.82 ( 618) link_BETA1-4 : bond 0.00213 / 0.11 ( 1) link_BETA1-4 : angle 2.33123 / 1.33 ( 3) link_NAG-ASN : bond 0.00453 / 0.24 ( 1) link_NAG-ASN : angle 0.96251 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.8758 (m-80) cc_final: 0.8311 (m-10) REVERT: A 237 LEU cc_start: 0.8737 (tp) cc_final: 0.8497 (tp) REVERT: A 260 MET cc_start: 0.7320 (mmp) cc_final: 0.6592 (ttp) REVERT: A 332 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 461 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8247 (mtt180) REVERT: A 595 TYR cc_start: 0.7185 (m-10) cc_final: 0.6686 (m-80) REVERT: A 606 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8901 (mm-30) REVERT: B 42 LYS cc_start: 0.8875 (tptt) cc_final: 0.8436 (tppt) REVERT: B 53 MET cc_start: 0.7759 (tpp) cc_final: 0.7211 (tmm) REVERT: B 59 ARG cc_start: 0.8297 (ttt180) cc_final: 0.7541 (ttm170) REVERT: B 120 TYR cc_start: 0.6754 (m-80) cc_final: 0.6323 (m-80) REVERT: B 127 MET cc_start: 0.9006 (mmp) cc_final: 0.8589 (mmp) REVERT: B 130 TRP cc_start: 0.8419 (m100) cc_final: 0.7925 (m100) REVERT: C 60 PHE cc_start: 0.7933 (m-80) cc_final: 0.7708 (m-80) REVERT: C 105 ASP cc_start: 0.8142 (m-30) cc_final: 0.7919 (m-30) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0787 time to fit residues: 17.7794 Evaluate side-chains 144 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 177 ASN B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.131169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.113635 restraints weight = 21068.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.116750 restraints weight = 13909.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118970 restraints weight = 10008.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.120578 restraints weight = 7657.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.121749 restraints weight = 6138.041| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6312 Z= 0.151 Angle : 0.636 9.458 8608 Z= 0.324 Chirality : 0.045 0.281 953 Planarity : 0.005 0.040 1050 Dihedral : 6.002 57.930 882 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.87 (0.30), residues: 759 helix: 0.42 (0.29), residues: 316 sheet: -0.85 (0.58), residues: 81 loop : -1.39 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 464 TYR 0.022 0.002 TYR A 410 PHE 0.019 0.002 PHE A 380 TRP 0.024 0.002 TRP A 253 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6307) covalent geometry : angle 0.63393 / 0.32 ( 8596) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 1.19209 / 0.59 ( 6) hydrogen bonds : bond 0.03841 / 2.52 ( 222) hydrogen bonds : angle 5.03488 / 3.77 ( 618) link_BETA1-4 : bond 0.00159 / 0.08 ( 1) link_BETA1-4 : angle 2.19279 / 1.25 ( 3) link_NAG-ASN : bond 0.00457 / 0.24 ( 1) link_NAG-ASN : angle 0.83613 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9166 (t80) cc_final: 0.8493 (t80) REVERT: A 158 PHE cc_start: 0.8761 (m-80) cc_final: 0.8371 (m-10) REVERT: A 237 LEU cc_start: 0.8799 (tp) cc_final: 0.8562 (tp) REVERT: A 260 MET cc_start: 0.7308 (mmp) cc_final: 0.6639 (ttp) REVERT: A 332 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 392 GLU cc_start: 0.8524 (tp30) cc_final: 0.7922 (tp30) REVERT: A 396 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7761 (mp0) REVERT: A 429 LEU cc_start: 0.8649 (mt) cc_final: 0.8413 (mt) REVERT: A 461 ARG cc_start: 0.8860 (mtt90) cc_final: 0.8303 (mtt180) REVERT: A 606 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8943 (mm-30) REVERT: B 42 LYS cc_start: 0.8896 (tptt) cc_final: 0.8338 (tppt) REVERT: B 59 ARG cc_start: 0.8416 (ttt180) cc_final: 0.8144 (ttt180) REVERT: B 84 LYS cc_start: 0.8519 (mppt) cc_final: 0.8092 (mmtm) REVERT: B 120 TYR cc_start: 0.6874 (m-80) cc_final: 0.6501 (m-80) REVERT: B 127 MET cc_start: 0.9052 (mmp) cc_final: 0.8606 (mmp) REVERT: B 130 TRP cc_start: 0.8525 (m100) cc_final: 0.8005 (m100) REVERT: C 60 PHE cc_start: 0.8077 (m-80) cc_final: 0.7824 (m-80) REVERT: C 105 ASP cc_start: 0.8070 (m-30) cc_final: 0.7823 (m-30) REVERT: C 107 THR cc_start: 0.8137 (p) cc_final: 0.7821 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0799 time to fit residues: 18.6159 Evaluate side-chains 146 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 72 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.118002 restraints weight = 20467.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.121503 restraints weight = 13100.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.124016 restraints weight = 9165.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.125828 restraints weight = 6843.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.127173 restraints weight = 5358.146| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6312 Z= 0.123 Angle : 0.628 9.419 8608 Z= 0.319 Chirality : 0.044 0.278 953 Planarity : 0.005 0.040 1050 Dihedral : 5.786 59.896 882 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.69 (0.30), residues: 759 helix: 0.41 (0.28), residues: 325 sheet: -0.64 (0.59), residues: 81 loop : -1.20 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 69 TYR 0.018 0.001 TYR A 410 PHE 0.019 0.001 PHE A 263 TRP 0.033 0.002 TRP B 52 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6307) covalent geometry : angle 0.62618 / 0.32 ( 8596) SS BOND : bond 0.00520 / 0.26 ( 3) SS BOND : angle 1.28930 / 0.66 ( 6) hydrogen bonds : bond 0.03638 / 2.36 ( 222) hydrogen bonds : angle 4.93077 / 3.63 ( 618) link_BETA1-4 : bond 0.00437 / 0.23 ( 1) link_BETA1-4 : angle 2.16451 / 1.23 ( 3) link_NAG-ASN : bond 0.00543 / 0.29 ( 1) link_NAG-ASN : angle 1.00957 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9068 (t80) cc_final: 0.8436 (t80) REVERT: A 158 PHE cc_start: 0.8688 (m-80) cc_final: 0.8291 (m-10) REVERT: A 237 LEU cc_start: 0.8764 (tp) cc_final: 0.8504 (tp) REVERT: A 260 MET cc_start: 0.7246 (mmp) cc_final: 0.6474 (ttp) REVERT: A 332 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 595 TYR cc_start: 0.7114 (m-10) cc_final: 0.6600 (m-80) REVERT: A 606 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8900 (mm-30) REVERT: B 42 LYS cc_start: 0.8898 (tptt) cc_final: 0.8521 (tppt) REVERT: B 59 ARG cc_start: 0.8325 (ttt180) cc_final: 0.8053 (ttt180) REVERT: B 84 LYS cc_start: 0.8420 (mppt) cc_final: 0.7964 (mmtm) REVERT: B 114 PHE cc_start: 0.7101 (m-80) cc_final: 0.6573 (m-80) REVERT: B 120 TYR cc_start: 0.6888 (m-80) cc_final: 0.6417 (m-80) REVERT: B 127 MET cc_start: 0.8956 (mmp) cc_final: 0.8616 (mmp) REVERT: B 130 TRP cc_start: 0.8440 (m100) cc_final: 0.7826 (m100) REVERT: C 105 ASP cc_start: 0.8089 (m-30) cc_final: 0.7845 (m-30) REVERT: C 107 THR cc_start: 0.8065 (p) cc_final: 0.7706 (t) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0769 time to fit residues: 17.6825 Evaluate side-chains 143 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 177 ASN B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.131988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.114057 restraints weight = 20599.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.117405 restraints weight = 13100.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.119713 restraints weight = 9209.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121404 restraints weight = 6975.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.122656 restraints weight = 5514.561| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.7538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6312 Z= 0.137 Angle : 0.630 9.268 8608 Z= 0.322 Chirality : 0.044 0.275 953 Planarity : 0.005 0.043 1050 Dihedral : 5.746 54.309 882 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.56 (0.31), residues: 759 helix: 0.55 (0.28), residues: 327 sheet: -0.43 (0.59), residues: 81 loop : -1.21 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 464 TYR 0.019 0.001 TYR A 410 PHE 0.017 0.002 PHE A 380 TRP 0.044 0.002 TRP A 537 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6307) covalent geometry : angle 0.62882 / 0.32 ( 8596) SS BOND : bond 0.00260 / 0.13 ( 3) SS BOND : angle 1.09269 / 0.55 ( 6) hydrogen bonds : bond 0.03604 / 2.36 ( 222) hydrogen bonds : angle 4.88543 / 3.60 ( 618) link_BETA1-4 : bond 0.00227 / 0.12 ( 1) link_BETA1-4 : angle 2.09479 / 1.20 ( 3) link_NAG-ASN : bond 0.00441 / 0.23 ( 1) link_NAG-ASN : angle 0.91937 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.9072 (m110) cc_final: 0.8831 (m110) REVERT: A 134 TYR cc_start: 0.9227 (t80) cc_final: 0.8504 (t80) REVERT: A 135 MET cc_start: 0.9207 (ttt) cc_final: 0.8825 (ttt) REVERT: A 158 PHE cc_start: 0.8655 (m-80) cc_final: 0.8366 (m-10) REVERT: A 237 LEU cc_start: 0.8762 (tp) cc_final: 0.8511 (tp) REVERT: A 260 MET cc_start: 0.7277 (mmp) cc_final: 0.6491 (ttp) REVERT: A 332 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 370 MET cc_start: 0.8931 (tpp) cc_final: 0.8301 (tmm) REVERT: A 528 MET cc_start: 0.8226 (mpp) cc_final: 0.8016 (mpp) REVERT: A 548 PHE cc_start: 0.7235 (m-10) cc_final: 0.7034 (m-10) REVERT: A 595 TYR cc_start: 0.7162 (m-10) cc_final: 0.6664 (m-80) REVERT: B 42 LYS cc_start: 0.8887 (tptt) cc_final: 0.8485 (tppt) REVERT: B 59 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8210 (ttt180) REVERT: B 114 PHE cc_start: 0.7271 (m-80) cc_final: 0.6653 (m-80) REVERT: B 120 TYR cc_start: 0.6846 (m-80) cc_final: 0.6397 (m-80) REVERT: B 127 MET cc_start: 0.9031 (mmp) cc_final: 0.8590 (mmp) REVERT: B 130 TRP cc_start: 0.8565 (m100) cc_final: 0.7881 (m100) REVERT: C 60 PHE cc_start: 0.8074 (m-80) cc_final: 0.7860 (m-80) REVERT: C 107 THR cc_start: 0.8147 (p) cc_final: 0.7804 (t) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0725 time to fit residues: 16.4890 Evaluate side-chains 139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 30 optimal weight: 0.0670 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.134374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116261 restraints weight = 20170.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.119663 restraints weight = 12906.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.122025 restraints weight = 9129.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.123784 restraints weight = 6853.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.125043 restraints weight = 5399.447| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.7645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6312 Z= 0.118 Angle : 0.610 9.298 8608 Z= 0.309 Chirality : 0.044 0.274 953 Planarity : 0.005 0.042 1050 Dihedral : 5.595 54.769 882 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.47 (0.31), residues: 759 helix: 0.63 (0.28), residues: 331 sheet: -0.32 (0.60), residues: 81 loop : -1.20 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 464 TYR 0.016 0.001 TYR A 410 PHE 0.024 0.002 PHE A 263 TRP 0.030 0.002 TRP A 537 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6307) covalent geometry : angle 0.60859 / 0.31 ( 8596) SS BOND : bond 0.00304 / 0.15 ( 3) SS BOND : angle 0.90353 / 0.46 ( 6) hydrogen bonds : bond 0.03514 / 2.28 ( 222) hydrogen bonds : angle 4.70662 / 3.44 ( 618) link_BETA1-4 : bond 0.00414 / 0.22 ( 1) link_BETA1-4 : angle 2.08862 / 1.19 ( 3) link_NAG-ASN : bond 0.00513 / 0.27 ( 1) link_NAG-ASN : angle 1.02030 / 0.60 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASN cc_start: 0.9003 (m110) cc_final: 0.8765 (m110) REVERT: A 135 MET cc_start: 0.9197 (ttt) cc_final: 0.8793 (ttt) REVERT: A 158 PHE cc_start: 0.8626 (m-80) cc_final: 0.8360 (m-10) REVERT: A 237 LEU cc_start: 0.8836 (tp) cc_final: 0.8551 (tp) REVERT: A 260 MET cc_start: 0.7008 (mmp) cc_final: 0.6191 (ttp) REVERT: A 289 TYR cc_start: 0.7907 (t80) cc_final: 0.7685 (t80) REVERT: A 461 ARG cc_start: 0.8734 (mtt90) cc_final: 0.8094 (mtt180) REVERT: A 595 TYR cc_start: 0.7083 (m-10) cc_final: 0.6540 (m-80) REVERT: B 42 LYS cc_start: 0.8920 (tptt) cc_final: 0.8504 (tppt) REVERT: B 59 ARG cc_start: 0.8411 (ttt180) cc_final: 0.8149 (ttt180) REVERT: B 84 LYS cc_start: 0.8325 (mppt) cc_final: 0.7927 (mmtm) REVERT: B 120 TYR cc_start: 0.6962 (m-80) cc_final: 0.6501 (m-80) REVERT: B 127 MET cc_start: 0.8976 (mmp) cc_final: 0.8552 (mmp) REVERT: C 107 THR cc_start: 0.8120 (p) cc_final: 0.7779 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0778 time to fit residues: 16.9232 Evaluate side-chains 137 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.108538 restraints weight = 21477.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.111596 restraints weight = 13884.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.113798 restraints weight = 9917.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.115303 restraints weight = 7522.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.116466 restraints weight = 6051.806| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6312 Z= 0.191 Angle : 0.698 9.423 8608 Z= 0.355 Chirality : 0.046 0.279 953 Planarity : 0.005 0.046 1050 Dihedral : 6.024 55.109 882 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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: -0.65 (0.31), residues: 759 helix: 0.56 (0.29), residues: 330 sheet: -0.42 (0.60), residues: 85 loop : -1.39 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 464 TYR 0.023 0.002 TYR A 410 PHE 0.017 0.002 PHE A 347 TRP 0.034 0.002 TRP A 537 HIS 0.004 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 6307) covalent geometry : angle 0.69575 / 0.35 ( 8596) SS BOND : bond 0.00352 / 0.17 ( 3) SS BOND : angle 1.21554 / 0.62 ( 6) hydrogen bonds : bond 0.03889 / 2.55 ( 222) hydrogen bonds : angle 5.02044 / 3.62 ( 618) link_BETA1-4 : bond 0.00863 / 0.45 ( 1) link_BETA1-4 : angle 2.38163 / 1.37 ( 3) link_NAG-ASN : bond 0.00415 / 0.22 ( 1) link_NAG-ASN : angle 0.74339 / 0.43 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.31 seconds wall clock time: 22 minutes 10.29 seconds (1330.29 seconds total)