Starting phenix.real_space_refine on Fri Sep 11 19:15:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xld_22240/09_2026/6xld_22240.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 20 5.16 5 C 7020 2.51 5 N 1804 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.01s 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: 10992 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4879 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 19, 'TRANS': 584} Chain breaks: 3 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.30, per 1000 atoms: 0.21 Number of scatterers: 10992 At special positions: 0 Unit cell: (99.546, 91.074, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1804 7.00 C 7020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 284.1 milliseconds 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 42.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 4.460A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 48 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.601A pdb=" N GLU A 57 " --> pdb=" O LYS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.512A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.771A pdb=" N LEU A 182 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 197 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.667A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 405 removed outlier: 3.994A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.652A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.906A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 459 removed outlier: 3.544A pdb=" N VAL A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 459' Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.656A pdb=" N VAL A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.969A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.844A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.535A pdb=" N ALA A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 removed outlier: 3.503A pdb=" N ILE A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.574A pdb=" N GLU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.830A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 627 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.562A pdb=" N LYS A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 removed outlier: 3.551A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.529A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 removed outlier: 3.560A pdb=" N LEU B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.569A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 removed outlier: 3.663A pdb=" N TYR B 184 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 186 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.857A pdb=" N ILE B 280 " --> pdb=" O PRO B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.652A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 405 removed outlier: 3.577A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.506A pdb=" N ASP B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.515A pdb=" N ILE B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 425 " --> pdb=" O ILE B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.795A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 removed outlier: 3.538A pdb=" N VAL B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 459' Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.599A pdb=" N VAL B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 removed outlier: 4.311A pdb=" N LEU B 487 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.549A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.699A pdb=" N LYS B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 555 removed outlier: 3.644A pdb=" N ASP B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.895A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 627 removed outlier: 3.765A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 651 removed outlier: 3.542A pdb=" N LYS B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 641 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 649 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 removed outlier: 3.591A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 4.101A pdb=" N GLU C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 244 removed outlier: 4.028A pdb=" N ALA C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 removed outlier: 3.678A pdb=" N GLU C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.839A pdb=" N ARG B 133 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 64 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU B 208 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE B 66 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.505A pdb=" N GLN A 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 265 removed outlier: 6.013A pdb=" N ILE A 64 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 208 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE A 66 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A 133 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 4 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.515A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 339 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.073A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 563 removed outlier: 3.570A pdb=" N ILE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.538A pdb=" N TYR B 301 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.979A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AB2, first strand: chain 'C' and resid 213 through 218 removed outlier: 5.710A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 259 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 213 through 218 removed outlier: 5.710A pdb=" N THR C 214 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 274 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 221 through 222 462 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3567 1.34 - 1.46: 2402 1.46 - 1.58: 5167 1.58 - 1.69: 10 1.69 - 1.81: 40 Bond restraints: 11186 Sorted by residual: bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 11181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 15059 3.44 - 6.88: 29 6.88 - 10.33: 6 10.33 - 13.77: 2 13.77 - 17.21: 2 Bond angle restraints: 15098 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.86 17.09 3.00e+00 1.11e-01 3.25e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.52 10.56 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.55 10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " pdb=" O2G ANP B 801 " ideal model delta sigma weight residual 101.05 109.64 -8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 15093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6595 17.67 - 35.34: 164 35.34 - 53.01: 28 53.01 - 70.67: 17 70.67 - 88.34: 15 Dihedral angle restraints: 6819 sinusoidal: 2855 harmonic: 3964 Sorted by residual: dihedral pdb=" CB GLU C 304 " pdb=" CG GLU C 304 " pdb=" CD GLU C 304 " pdb=" OE1 GLU C 304 " ideal model delta sinusoidal sigma weight residual 0.00 -88.34 88.34 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 351 " pdb=" CG GLU B 351 " pdb=" CD GLU B 351 " pdb=" OE1 GLU B 351 " ideal model delta sinusoidal sigma weight residual 0.00 87.70 -87.70 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 462 " pdb=" CG GLU B 462 " pdb=" CD GLU B 462 " pdb=" OE1 GLU B 462 " ideal model delta sinusoidal sigma weight residual 0.00 -86.37 86.37 1 3.00e+01 1.11e-03 9.99e+00 ... (remaining 6816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1486 0.055 - 0.109: 194 0.109 - 0.164: 19 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1701 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1698 not shown) Planarity restraints: 1923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 355 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 570 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.62e-01 pdb=" N PRO B 571 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 571 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 571 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 544 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.94e-01 pdb=" N PRO A 545 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 545 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 545 " 0.013 5.00e-02 4.00e+02 ... (remaining 1920 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 134 2.63 - 3.20: 9453 3.20 - 3.76: 16764 3.76 - 4.33: 24482 4.33 - 4.90: 39640 Nonbonded interactions: 90473 Sorted by model distance: nonbonded pdb=" O1B ANP A 801 " pdb="MG MG A 802 " model vdw 2.061 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.107 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.131 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.141 2.170 nonbonded pdb=" OD1 ASN A 37 " pdb="MG MG A 802 " model vdw 2.166 2.170 ... (remaining 90468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 323 or resid 335 through 802)) selection = chain 'B' } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.550 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 11186 Z= 0.167 Angle : 0.507 17.210 15098 Z= 0.243 Chirality : 0.039 0.273 1701 Planarity : 0.003 0.034 1923 Dihedral : 9.938 88.343 4235 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.58 % Allowed : 3.31 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.19), residues: 1331 helix: -3.74 (0.12), residues: 513 sheet: -1.24 (0.31), residues: 272 loop : -1.60 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 169 TYR 0.005 0.001 TYR B 285 PHE 0.004 0.001 PHE A 609 TRP 0.006 0.001 TRP A 273 HIS 0.001 0.000 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (11186) covalent geometry : angle 0.50666 / 0.24 (15098) hydrogen bonds : bond 0.29697 / 19.05 ( 446) hydrogen bonds : angle 9.26925 / 6.32 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 294 time to evaluate : 0.376 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 207 LEU cc_start: 0.8068 (tp) cc_final: 0.7806 (tp) REVERT: C 223 ASN cc_start: 0.7570 (t0) cc_final: 0.7337 (p0) outliers start: 7 outliers final: 1 residues processed: 299 average time/residue: 0.1234 time to fit residues: 49.0793 Evaluate side-chains 124 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 92 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 640 ASN B 9 GLN B 55 GLN B 197 HIS B 442 ASN B 557 GLN B 640 ASN C 237 GLN C 284 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.081854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071392 restraints weight = 35273.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073271 restraints weight = 20300.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.074559 restraints weight = 13941.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075309 restraints weight = 10603.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075987 restraints weight = 8819.448| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 11186 Z= 0.269 Angle : 0.712 8.258 15098 Z= 0.367 Chirality : 0.048 0.166 1701 Planarity : 0.005 0.045 1923 Dihedral : 5.189 68.606 1449 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.40 % Allowed : 9.93 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.21), residues: 1331 helix: -1.48 (0.20), residues: 521 sheet: -1.27 (0.29), residues: 259 loop : -0.89 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 238 TYR 0.019 0.002 TYR A 125 PHE 0.020 0.002 PHE B 8 TRP 0.016 0.002 TRP A 357 HIS 0.004 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (11186) covalent geometry : angle 0.71227 / 0.37 (15098) hydrogen bonds : bond 0.04202 / 2.78 ( 446) hydrogen bonds : angle 5.66291 / 3.91 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8761 (mtm) cc_final: 0.8516 (mtt) REVERT: B 64 ILE cc_start: 0.8621 (mm) cc_final: 0.8419 (mm) REVERT: B 84 MET cc_start: 0.7974 (mtp) cc_final: 0.7748 (mtp) REVERT: B 136 VAL cc_start: 0.8049 (t) cc_final: 0.7848 (t) REVERT: B 180 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7238 (p0) REVERT: B 381 GLN cc_start: 0.7004 (mp10) cc_final: 0.6727 (mp10) REVERT: B 649 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8670 (t) REVERT: B 650 SER cc_start: 0.8875 (m) cc_final: 0.8591 (t) outliers start: 29 outliers final: 15 residues processed: 142 average time/residue: 0.1090 time to fit residues: 21.9776 Evaluate side-chains 91 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 126 optimal weight: 0.0040 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.084098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073819 restraints weight = 35016.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075731 restraints weight = 20435.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077053 restraints weight = 14038.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.077949 restraints weight = 10666.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.078570 restraints weight = 8674.570| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11186 Z= 0.118 Angle : 0.531 7.214 15098 Z= 0.273 Chirality : 0.043 0.198 1701 Planarity : 0.003 0.039 1923 Dihedral : 4.809 73.588 1448 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 12.16 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1331 helix: -0.40 (0.23), residues: 523 sheet: -0.96 (0.30), residues: 264 loop : -0.62 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 536 TYR 0.022 0.001 TYR B 289 PHE 0.013 0.001 PHE A 660 TRP 0.013 0.001 TRP A 148 HIS 0.002 0.000 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11186) covalent geometry : angle 0.53129 / 0.27 (15098) hydrogen bonds : bond 0.03427 / 2.23 ( 446) hydrogen bonds : angle 5.07151 / 3.46 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ILE cc_start: 0.8407 (mm) cc_final: 0.8189 (mm) REVERT: B 381 GLN cc_start: 0.6909 (mp10) cc_final: 0.6677 (mp10) REVERT: B 650 SER cc_start: 0.8883 (m) cc_final: 0.8562 (t) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 0.0912 time to fit residues: 15.3471 Evaluate side-chains 84 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 107 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.0010 chunk 38 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 373 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.086258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075956 restraints weight = 34882.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.077929 restraints weight = 20191.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079266 restraints weight = 13788.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080152 restraints weight = 10465.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080806 restraints weight = 8532.077| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11186 Z= 0.088 Angle : 0.490 8.440 15098 Z= 0.250 Chirality : 0.042 0.159 1701 Planarity : 0.003 0.038 1923 Dihedral : 4.603 74.582 1448 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 12.57 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1331 helix: 0.05 (0.23), residues: 526 sheet: -0.53 (0.31), residues: 264 loop : -0.40 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.016 0.001 TYR B 289 PHE 0.015 0.001 PHE A 660 TRP 0.014 0.001 TRP B 148 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (11186) covalent geometry : angle 0.48988 / 0.25 (15098) hydrogen bonds : bond 0.02978 / 1.93 ( 446) hydrogen bonds : angle 4.73008 / 3.21 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ILE cc_start: 0.8203 (mm) cc_final: 0.8000 (mm) REVERT: B 585 MET cc_start: 0.8458 (tpp) cc_final: 0.8249 (tpp) REVERT: B 650 SER cc_start: 0.8820 (m) cc_final: 0.8515 (t) REVERT: C 230 TYR cc_start: 0.7935 (t80) cc_final: 0.7287 (t80) REVERT: C 324 GLU cc_start: 0.6087 (mp0) cc_final: 0.5860 (mp0) outliers start: 13 outliers final: 7 residues processed: 111 average time/residue: 0.0859 time to fit residues: 14.9254 Evaluate side-chains 89 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.073087 restraints weight = 34911.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074988 restraints weight = 20336.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076310 restraints weight = 14004.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077220 restraints weight = 10666.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077754 restraints weight = 8707.617| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11186 Z= 0.128 Angle : 0.516 8.121 15098 Z= 0.263 Chirality : 0.043 0.165 1701 Planarity : 0.003 0.038 1923 Dihedral : 4.700 75.557 1448 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.49 % Allowed : 13.40 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1331 helix: 0.31 (0.23), residues: 532 sheet: -0.51 (0.31), residues: 262 loop : -0.43 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.017 0.001 TYR B 289 PHE 0.012 0.001 PHE A 660 TRP 0.014 0.001 TRP B 148 HIS 0.001 0.000 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11186) covalent geometry : angle 0.51571 / 0.26 (15098) hydrogen bonds : bond 0.02967 / 1.90 ( 446) hydrogen bonds : angle 4.73065 / 3.21 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8095 (mmm) cc_final: 0.7712 (mmm) REVERT: A 43 ASP cc_start: 0.7890 (m-30) cc_final: 0.7548 (m-30) REVERT: B 650 SER cc_start: 0.8896 (m) cc_final: 0.8603 (t) REVERT: C 230 TYR cc_start: 0.8029 (t80) cc_final: 0.7361 (t80) outliers start: 18 outliers final: 9 residues processed: 103 average time/residue: 0.0851 time to fit residues: 13.7192 Evaluate side-chains 84 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 19 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 31 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.084178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073883 restraints weight = 34909.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075825 restraints weight = 20320.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.077161 restraints weight = 13921.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078017 restraints weight = 10565.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078672 restraints weight = 8656.971| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11186 Z= 0.101 Angle : 0.498 8.780 15098 Z= 0.254 Chirality : 0.042 0.183 1701 Planarity : 0.003 0.038 1923 Dihedral : 4.688 76.268 1448 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.57 % Allowed : 13.48 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1331 helix: 0.45 (0.23), residues: 538 sheet: -0.46 (0.32), residues: 262 loop : -0.45 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.019 0.001 TYR B 289 PHE 0.017 0.001 PHE A 512 TRP 0.015 0.001 TRP B 148 HIS 0.001 0.000 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (11186) covalent geometry : angle 0.49794 / 0.25 (15098) hydrogen bonds : bond 0.02808 / 1.81 ( 446) hydrogen bonds : angle 4.59763 / 3.12 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7942 (m-30) cc_final: 0.7673 (m-30) REVERT: B 650 SER cc_start: 0.8779 (m) cc_final: 0.8520 (t) REVERT: C 230 TYR cc_start: 0.8025 (t80) cc_final: 0.7356 (t80) outliers start: 19 outliers final: 9 residues processed: 115 average time/residue: 0.0829 time to fit residues: 14.7431 Evaluate side-chains 89 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.0010 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.083185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072740 restraints weight = 34725.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074637 restraints weight = 20335.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075986 restraints weight = 14074.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076782 restraints weight = 10716.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077450 restraints weight = 8883.766| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11186 Z= 0.117 Angle : 0.514 9.216 15098 Z= 0.262 Chirality : 0.043 0.181 1701 Planarity : 0.003 0.038 1923 Dihedral : 4.750 76.001 1448 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.65 % Allowed : 14.39 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1331 helix: 0.52 (0.23), residues: 536 sheet: -0.50 (0.31), residues: 273 loop : -0.41 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.021 0.001 TYR B 289 PHE 0.011 0.001 PHE A 6 TRP 0.020 0.002 TRP B 148 HIS 0.001 0.000 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11186) covalent geometry : angle 0.51389 / 0.26 (15098) hydrogen bonds : bond 0.02912 / 1.88 ( 446) hydrogen bonds : angle 4.63758 / 3.16 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7933 (m-30) cc_final: 0.7656 (m-30) REVERT: B 650 SER cc_start: 0.8816 (m) cc_final: 0.8577 (t) REVERT: C 230 TYR cc_start: 0.8036 (t80) cc_final: 0.7330 (t80) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.0894 time to fit residues: 13.9772 Evaluate side-chains 90 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 68 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.083507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073131 restraints weight = 34546.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075049 restraints weight = 20154.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076390 restraints weight = 13900.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077244 restraints weight = 10564.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.077901 restraints weight = 8667.268| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11186 Z= 0.106 Angle : 0.522 10.391 15098 Z= 0.262 Chirality : 0.043 0.191 1701 Planarity : 0.003 0.038 1923 Dihedral : 4.750 76.447 1448 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.91 % Allowed : 14.64 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1331 helix: 0.50 (0.23), residues: 538 sheet: -0.55 (0.31), residues: 275 loop : -0.32 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.016 0.001 TYR B 289 PHE 0.016 0.001 PHE A 512 TRP 0.021 0.002 TRP B 148 HIS 0.001 0.000 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11186) covalent geometry : angle 0.52160 / 0.26 (15098) hydrogen bonds : bond 0.02815 / 1.81 ( 446) hydrogen bonds : angle 4.56163 / 3.10 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7929 (m-30) cc_final: 0.7645 (m-30) REVERT: B 650 SER cc_start: 0.8716 (m) cc_final: 0.8486 (t) REVERT: C 230 TYR cc_start: 0.8033 (t80) cc_final: 0.7324 (t80) outliers start: 11 outliers final: 11 residues processed: 95 average time/residue: 0.0916 time to fit residues: 13.2156 Evaluate side-chains 90 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 15 optimal weight: 0.0470 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 overall best weight: 0.7892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.084066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073735 restraints weight = 34441.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075646 restraints weight = 20161.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.076990 restraints weight = 13915.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077741 restraints weight = 10562.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.078464 restraints weight = 8794.500| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11186 Z= 0.095 Angle : 0.506 10.127 15098 Z= 0.256 Chirality : 0.042 0.186 1701 Planarity : 0.003 0.040 1923 Dihedral : 4.708 75.456 1448 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.99 % Allowed : 14.97 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1331 helix: 0.52 (0.24), residues: 538 sheet: -0.58 (0.32), residues: 270 loop : -0.31 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 663 TYR 0.023 0.001 TYR B 289 PHE 0.021 0.001 PHE A 512 TRP 0.022 0.002 TRP B 148 HIS 0.001 0.000 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (11186) covalent geometry : angle 0.50633 / 0.26 (15098) hydrogen bonds : bond 0.02764 / 1.78 ( 446) hydrogen bonds : angle 4.54314 / 3.08 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7926 (m-30) cc_final: 0.7638 (m-30) REVERT: A 105 MET cc_start: 0.8603 (tpp) cc_final: 0.8366 (mmt) REVERT: B 148 TRP cc_start: 0.7438 (t60) cc_final: 0.7208 (t60) REVERT: B 650 SER cc_start: 0.8702 (m) cc_final: 0.8493 (t) REVERT: C 230 TYR cc_start: 0.8040 (t80) cc_final: 0.7299 (t80) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.0901 time to fit residues: 13.3954 Evaluate side-chains 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.083803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073532 restraints weight = 34687.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075438 restraints weight = 20128.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076772 restraints weight = 13849.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.077670 restraints weight = 10484.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078281 restraints weight = 8517.651| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11186 Z= 0.101 Angle : 0.526 11.384 15098 Z= 0.262 Chirality : 0.042 0.196 1701 Planarity : 0.003 0.040 1923 Dihedral : 4.714 75.829 1448 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.74 % Allowed : 15.63 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1331 helix: 0.54 (0.24), residues: 537 sheet: -0.52 (0.31), residues: 277 loop : -0.27 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 663 TYR 0.022 0.001 TYR B 289 PHE 0.018 0.001 PHE A 6 TRP 0.025 0.002 TRP C 317 HIS 0.001 0.000 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (11186) covalent geometry : angle 0.52600 / 0.26 (15098) hydrogen bonds : bond 0.02786 / 1.78 ( 446) hydrogen bonds : angle 4.52349 / 3.07 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7945 (m-30) cc_final: 0.7648 (m-30) REVERT: B 148 TRP cc_start: 0.7480 (t60) cc_final: 0.7260 (t60) REVERT: B 650 SER cc_start: 0.8710 (m) cc_final: 0.8503 (t) REVERT: C 230 TYR cc_start: 0.8037 (t80) cc_final: 0.7303 (t80) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.0934 time to fit residues: 12.7584 Evaluate side-chains 84 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.0270 chunk 51 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.085950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075744 restraints weight = 34314.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077698 restraints weight = 19846.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079020 restraints weight = 13555.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079850 restraints weight = 10255.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080553 restraints weight = 8422.290| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11186 Z= 0.085 Angle : 0.512 10.907 15098 Z= 0.255 Chirality : 0.042 0.186 1701 Planarity : 0.003 0.040 1923 Dihedral : 4.568 72.359 1448 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.83 % Allowed : 15.63 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1331 helix: 0.58 (0.24), residues: 534 sheet: -0.33 (0.32), residues: 272 loop : -0.26 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.022 0.001 TYR B 289 PHE 0.018 0.001 PHE A 6 TRP 0.026 0.002 TRP C 317 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (11186) covalent geometry : angle 0.51233 / 0.25 (15098) hydrogen bonds : bond 0.02658 / 1.69 ( 446) hydrogen bonds : angle 4.38197 / 2.98 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1514.09 seconds wall clock time: 27 minutes 13.06 seconds (1633.06 seconds total)