Starting phenix.real_space_refine on Wed Mar 4 05:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xld_22240/03_2026/6xld_22240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xld_22240/03_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_22240/03_2026/6xld_22240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xld_22240/03_2026/6xld_22240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xld_22240/03_2026/6xld_22240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xld_22240/03_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-dev-5986/lib/python3.9/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: 2.44, per 1000 atoms: 0.22 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: 0.81 Conformation dependent library (CDL) restraints added in 403.9 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: 0.33 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: 1.90 Time building geometry restraints manager: 1.08 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: 6638 17.67 - 35.34: 172 35.34 - 53.01: 31 53.01 - 70.67: 17 70.67 - 88.34: 17 Dihedral angle restraints: 6875 sinusoidal: 2911 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 6872 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: 1.370 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.310 Find NCS groups from input model: 0.160 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 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 : 10.186 88.343 4291 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 covalent geometry : bond 0.00330 (11186) covalent geometry : angle 0.50666 (15098) hydrogen bonds : bond 0.29697 ( 446) hydrogen bonds : angle 9.26925 ( 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 : 0.397 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: 0.1253 time to fit residues: 49.6063 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 : 0.387 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3459 r_free = 0.3459 target = 0.082114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071560 restraints weight = 35277.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073450 restraints weight = 20436.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074746 restraints weight = 14067.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.075624 restraints weight = 10738.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076185 restraints weight = 8783.836| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 11186 Z= 0.264 Angle : 0.702 8.055 15098 Z= 0.361 Chirality : 0.048 0.173 1701 Planarity : 0.005 0.046 1923 Dihedral : 6.416 70.204 1505 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.40 % Allowed : 10.09 % Favored : 87.51 % 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: -1.99 (0.21), residues: 1331 helix: -1.51 (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 0.019 0.002 PHE B 8 TRP 0.015 0.002 TRP A 357 HIS 0.004 0.002 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00605 (11186) covalent geometry : angle 0.70221 (15098) hydrogen bonds : bond 0.04369 ( 446) hydrogen bonds : angle 5.67896 ( 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 146 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8750 (mtm) cc_final: 0.8502 (mtt) REVERT: B 64 ILE cc_start: 0.8608 (mm) cc_final: 0.8402 (mm) REVERT: B 84 MET cc_start: 0.7955 (mtp) cc_final: 0.7723 (mtp) REVERT: B 136 VAL cc_start: 0.8051 (t) cc_final: 0.7837 (t) REVERT: B 180 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7215 (p0) REVERT: B 381 GLN cc_start: 0.7022 (mp10) cc_final: 0.6733 (mp10) outliers start: 29 outliers final: 14 residues processed: 141 average time/residue: 0.1048 time to fit residues: 20.9833 Evaluate side-chains 87 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 0.0870 chunk 124 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.084407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074125 restraints weight = 34950.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.076048 restraints weight = 20378.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077365 restraints weight = 13983.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078278 restraints weight = 10616.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078840 restraints weight = 8624.780| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11186 Z= 0.115 Angle : 0.527 7.151 15098 Z= 0.272 Chirality : 0.043 0.197 1701 Planarity : 0.003 0.039 1923 Dihedral : 5.937 74.427 1504 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.24 % Allowed : 11.99 % 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: -0.38 (0.23), residues: 523 sheet: -0.95 (0.30), residues: 264 loop : -0.63 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 174 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 covalent geometry : bond 0.00267 (11186) covalent geometry : angle 0.52721 (15098) hydrogen bonds : bond 0.03405 ( 446) hydrogen bonds : angle 5.06693 ( 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 119 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8060 (mmm) cc_final: 0.7729 (mmm) REVERT: B 64 ILE cc_start: 0.8423 (mm) cc_final: 0.8209 (mm) REVERT: B 381 GLN cc_start: 0.6895 (mp10) cc_final: 0.6670 (mp10) REVERT: B 650 SER cc_start: 0.8877 (m) cc_final: 0.8455 (p) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.0900 time to fit residues: 15.2374 Evaluate side-chains 87 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 550 LEU 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: 9.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 373 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074286 restraints weight = 35029.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076245 restraints weight = 20319.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077482 restraints weight = 13879.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078435 restraints weight = 10705.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079030 restraints weight = 8677.553| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11186 Z= 0.103 Angle : 0.504 8.888 15098 Z= 0.257 Chirality : 0.042 0.166 1701 Planarity : 0.003 0.039 1923 Dihedral : 5.863 74.036 1504 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.24 % Allowed : 12.90 % Favored : 85.86 % 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: -0.56 (0.23), residues: 1331 helix: 0.07 (0.23), residues: 526 sheet: -0.65 (0.32), residues: 249 loop : -0.48 (0.26), residues: 556 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 0.014 0.001 PHE A 512 TRP 0.014 0.001 TRP B 148 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00242 (11186) covalent geometry : angle 0.50383 (15098) hydrogen bonds : bond 0.03026 ( 446) hydrogen bonds : angle 4.81244 ( 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 109 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ILE cc_start: 0.8310 (mm) cc_final: 0.8106 (mm) REVERT: B 385 MET cc_start: 0.6867 (tmm) cc_final: 0.6599 (ptt) REVERT: B 650 SER cc_start: 0.8873 (m) cc_final: 0.8455 (p) REVERT: C 230 TYR cc_start: 0.7969 (t80) cc_final: 0.7348 (t80) REVERT: C 301 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7537 (p) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.0824 time to fit residues: 13.3782 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 : 0.412 ------------------------------------------------------------------------------- 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 453 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 106 optimal weight: 0.0170 chunk 13 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072433 restraints weight = 34897.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074321 restraints weight = 20313.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075657 restraints weight = 14017.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076559 restraints weight = 10659.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077133 restraints weight = 8697.695| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11186 Z= 0.132 Angle : 0.518 7.200 15098 Z= 0.264 Chirality : 0.043 0.165 1701 Planarity : 0.003 0.038 1923 Dihedral : 5.921 75.525 1504 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.74 % Allowed : 13.90 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1331 helix: 0.28 (0.23), residues: 535 sheet: -0.69 (0.32), residues: 249 loop : -0.49 (0.26), residues: 547 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 0.002 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00307 (11186) covalent geometry : angle 0.51845 (15098) hydrogen bonds : bond 0.03027 ( 446) hydrogen bonds : angle 4.78168 ( 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 106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7896 (mmm) cc_final: 0.7635 (mmm) REVERT: B 487 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9222 (mm) REVERT: C 230 TYR cc_start: 0.7994 (t80) cc_final: 0.7380 (t80) REVERT: C 301 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7603 (p) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.0919 time to fit residues: 14.1287 Evaluate side-chains 86 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 316 ILE 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 A residue 550 LEU 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 B residue 487 LEU 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: 6.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.083434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.073011 restraints weight = 35082.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074921 restraints weight = 20385.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076267 restraints weight = 14052.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.077171 restraints weight = 10691.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077742 restraints weight = 8719.904| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11186 Z= 0.106 Angle : 0.505 8.907 15098 Z= 0.257 Chirality : 0.042 0.144 1701 Planarity : 0.003 0.038 1923 Dihedral : 5.854 75.349 1504 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.57 % Allowed : 14.72 % Favored : 83.71 % 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: -0.30 (0.23), residues: 1331 helix: 0.44 (0.23), residues: 536 sheet: -0.57 (0.32), residues: 261 loop : -0.49 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.018 0.001 TYR B 289 PHE 0.018 0.001 PHE A 512 TRP 0.019 0.001 TRP B 148 HIS 0.001 0.000 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00246 (11186) covalent geometry : angle 0.50529 (15098) hydrogen bonds : bond 0.02840 ( 446) hydrogen bonds : angle 4.63453 ( 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 111 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 TYR cc_start: 0.7997 (t80) cc_final: 0.7355 (t80) REVERT: C 301 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7632 (p) outliers start: 19 outliers final: 9 residues processed: 107 average time/residue: 0.0816 time to fit residues: 13.3574 Evaluate side-chains 87 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL 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 A residue 550 LEU 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: 6.9990 chunk 17 optimal weight: 7.9990 chunk 65 optimal weight: 0.0070 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3442 r_free = 0.3442 target = 0.081596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071252 restraints weight = 34955.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.073127 restraints weight = 20332.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074443 restraints weight = 14022.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075253 restraints weight = 10667.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075931 restraints weight = 8806.699| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11186 Z= 0.151 Angle : 0.538 9.069 15098 Z= 0.276 Chirality : 0.043 0.168 1701 Planarity : 0.003 0.039 1923 Dihedral : 5.987 76.596 1504 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.57 % Allowed : 14.81 % 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: -0.34 (0.23), residues: 1331 helix: 0.44 (0.23), residues: 541 sheet: -0.75 (0.32), residues: 260 loop : -0.47 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.019 0.001 TYR B 289 PHE 0.011 0.001 PHE B 579 TRP 0.017 0.002 TRP B 148 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00354 (11186) covalent geometry : angle 0.53810 (15098) hydrogen bonds : bond 0.03037 ( 446) hydrogen bonds : angle 4.77005 ( 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 103 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7237 (p0) REVERT: C 301 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7630 (p) REVERT: C 324 GLU cc_start: 0.6220 (mp0) cc_final: 0.5955 (mp0) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.1015 time to fit residues: 14.9124 Evaluate side-chains 88 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 316 ILE 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 A residue 550 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 339 LEU 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: 0.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 0.0050 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 0.0050 chunk 129 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074293 restraints weight = 34455.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076228 restraints weight = 19963.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077578 restraints weight = 13700.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078412 restraints weight = 10368.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079108 restraints weight = 8501.388| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5556 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= 0.087 Angle : 0.502 10.176 15098 Z= 0.252 Chirality : 0.042 0.182 1701 Planarity : 0.003 0.040 1923 Dihedral : 5.773 74.741 1504 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.08 % Allowed : 14.97 % 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: -0.21 (0.23), residues: 1331 helix: 0.48 (0.23), residues: 539 sheet: -0.61 (0.32), residues: 265 loop : -0.35 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.017 0.001 TYR B 289 PHE 0.012 0.001 PHE A 512 TRP 0.021 0.002 TRP B 148 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00192 (11186) covalent geometry : angle 0.50239 (15098) hydrogen bonds : bond 0.02703 ( 446) hydrogen bonds : angle 4.52161 ( 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 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8543 (tpp) cc_final: 0.8313 (mmt) REVERT: C 230 TYR cc_start: 0.8005 (t80) cc_final: 0.7300 (t80) REVERT: C 301 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7594 (p) outliers start: 13 outliers final: 7 residues processed: 107 average time/residue: 0.0853 time to fit residues: 14.2210 Evaluate side-chains 88 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 550 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 354 ILE 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: 2.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.081839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071496 restraints weight = 34595.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073383 restraints weight = 20168.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074682 restraints weight = 13881.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075482 restraints weight = 10597.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076114 restraints weight = 8782.075| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.5759 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= 0.144 Angle : 0.542 10.803 15098 Z= 0.274 Chirality : 0.044 0.200 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.891 76.955 1504 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.16 % Allowed : 15.80 % Favored : 83.04 % 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: -0.22 (0.23), residues: 1331 helix: 0.54 (0.23), residues: 537 sheet: -0.71 (0.32), residues: 268 loop : -0.37 (0.26), residues: 526 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 0.019 0.001 PHE B 63 TRP 0.024 0.002 TRP C 317 HIS 0.002 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00336 (11186) covalent geometry : angle 0.54221 (15098) hydrogen bonds : bond 0.02956 ( 446) hydrogen bonds : angle 4.65425 ( 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 91 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 TRP cc_start: 0.7550 (t60) cc_final: 0.7344 (t60) REVERT: B 180 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7199 (p0) REVERT: C 230 TYR cc_start: 0.8116 (t80) cc_final: 0.7392 (t80) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.0940 time to fit residues: 12.3948 Evaluate side-chains 84 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 316 ILE 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 A residue 550 LEU 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 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.082293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071987 restraints weight = 34760.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073869 restraints weight = 20112.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075186 restraints weight = 13847.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076006 restraints weight = 10522.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076689 restraints weight = 8666.902| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11186 Z= 0.122 Angle : 0.541 10.663 15098 Z= 0.270 Chirality : 0.043 0.194 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.912 77.703 1504 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.74 % Allowed : 16.29 % Favored : 82.96 % 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: -0.22 (0.23), residues: 1331 helix: 0.49 (0.23), residues: 539 sheet: -0.68 (0.32), residues: 268 loop : -0.34 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 65 TYR 0.022 0.001 TYR B 289 PHE 0.022 0.001 PHE A 512 TRP 0.026 0.002 TRP C 317 HIS 0.011 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00285 (11186) covalent geometry : angle 0.54118 (15098) hydrogen bonds : bond 0.02876 ( 446) hydrogen bonds : angle 4.63334 ( 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 85 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.7140 (mmpt) cc_final: 0.6846 (mtmm) REVERT: B 148 TRP cc_start: 0.7479 (t60) cc_final: 0.7275 (t60) REVERT: C 230 TYR cc_start: 0.8119 (t80) cc_final: 0.7402 (t80) outliers start: 9 outliers final: 9 residues processed: 82 average time/residue: 0.0896 time to fit residues: 11.2429 Evaluate side-chains 82 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 316 ILE 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 A residue 550 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 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 = 0.3480 r_free = 0.3480 target = 0.083460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073243 restraints weight = 34460.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075149 restraints weight = 19870.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076474 restraints weight = 13606.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077257 restraints weight = 10300.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.077952 restraints weight = 8509.427| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5904 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= 0.100 Angle : 0.528 10.481 15098 Z= 0.264 Chirality : 0.043 0.194 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.823 76.459 1504 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.08 % Allowed : 16.29 % Favored : 82.63 % 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: -0.15 (0.23), residues: 1331 helix: 0.60 (0.24), residues: 539 sheet: -0.62 (0.32), residues: 268 loop : -0.37 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 65 TYR 0.022 0.001 TYR B 289 PHE 0.015 0.001 PHE A 6 TRP 0.023 0.002 TRP C 317 HIS 0.006 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00230 (11186) covalent geometry : angle 0.52841 (15098) hydrogen bonds : bond 0.02766 ( 446) hydrogen bonds : angle 4.58643 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.00 seconds wall clock time: 26 minutes 14.59 seconds (1574.59 seconds total)