Starting phenix.real_space_refine on Tue Jul 29 07:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xld_22240/07_2025/6xld_22240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xld_22240/07_2025/6xld_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xld_22240/07_2025/6xld_22240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xld_22240/07_2025/6xld_22240.map" model { file = "/net/cci-nas-00/data/ceres_data/6xld_22240/07_2025/6xld_22240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xld_22240/07_2025/6xld_22240.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.60, per 1000 atoms: 0.60 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: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.39 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: 4.23 Time building geometry restraints manager: 2.77 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 675 or resid 801 throug \ h 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: 0.960 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.330 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (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 TRP 0.006 0.001 TRP A 273 HIS 0.001 0.000 HIS A 463 PHE 0.004 0.001 PHE A 609 TYR 0.005 0.001 TYR B 285 ARG 0.001 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.29697 ( 446) hydrogen bonds : angle 9.26925 ( 1275) covalent geometry : bond 0.00330 (11186) covalent geometry : angle 0.50666 (15098) *********************** 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 : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.3032 time to fit residues: 119.1377 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 : 1.332 ------------------------------------------------------------------------------- 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 112 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 261 GLN A 380 GLN 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 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.087838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077262 restraints weight = 34792.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079261 restraints weight = 19995.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.080672 restraints weight = 13645.318| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11186 Z= 0.161 Angle : 0.585 7.743 15098 Z= 0.299 Chirality : 0.044 0.167 1701 Planarity : 0.004 0.037 1923 Dihedral : 5.812 69.393 1505 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.15 % Allowed : 9.43 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.21), residues: 1331 helix: -1.55 (0.20), residues: 523 sheet: -1.13 (0.28), residues: 272 loop : -0.84 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 357 HIS 0.004 0.001 HIS B 197 PHE 0.017 0.002 PHE A 660 TYR 0.016 0.002 TYR A 441 ARG 0.006 0.001 ARG C 238 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 446) hydrogen bonds : angle 5.48280 ( 1275) covalent geometry : bond 0.00371 (11186) covalent geometry : angle 0.58512 (15098) *********************** 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 162 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 LEU cc_start: 0.9203 (mt) cc_final: 0.8998 (mt) REVERT: B 84 MET cc_start: 0.7975 (mtp) cc_final: 0.7604 (mtp) REVERT: B 180 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6932 (p0) REVERT: B 381 GLN cc_start: 0.6731 (mp10) cc_final: 0.6485 (mp10) outliers start: 26 outliers final: 12 residues processed: 158 average time/residue: 0.2633 time to fit residues: 58.2934 Evaluate side-chains 103 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 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 641 LEU Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 342 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 0.0570 chunk 123 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- 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 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN C 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.080521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.070200 restraints weight = 35495.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072078 restraints weight = 20695.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073343 restraints weight = 14194.851| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 11186 Z= 0.243 Angle : 0.658 8.570 15098 Z= 0.340 Chirality : 0.046 0.263 1701 Planarity : 0.004 0.040 1923 Dihedral : 6.315 74.228 1504 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.15 % Allowed : 12.41 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1331 helix: -0.38 (0.22), residues: 523 sheet: -0.98 (0.30), residues: 261 loop : -0.75 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 148 HIS 0.003 0.001 HIS B 463 PHE 0.021 0.002 PHE A 512 TYR 0.014 0.002 TYR A 285 ARG 0.011 0.001 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 446) hydrogen bonds : angle 5.37294 ( 1275) covalent geometry : bond 0.00561 (11186) covalent geometry : angle 0.65780 (15098) *********************** 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 124 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.8652 (mtm) cc_final: 0.8418 (mtt) REVERT: A 396 LEU cc_start: 0.9240 (mt) cc_final: 0.8993 (mt) REVERT: A 512 PHE cc_start: 0.8253 (t80) cc_final: 0.7947 (t80) REVERT: B 84 MET cc_start: 0.7995 (mtp) cc_final: 0.7749 (mtp) REVERT: B 180 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7196 (p0) REVERT: B 381 GLN cc_start: 0.7036 (mp10) cc_final: 0.6720 (mp10) REVERT: B 649 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8619 (t) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.2356 time to fit residues: 40.7729 Evaluate side-chains 90 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 122 VAL 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 460 MET 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 455 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain C residue 224 VAL 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 98 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 131 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.083663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073428 restraints weight = 34498.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075320 restraints weight = 20067.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076648 restraints weight = 13818.641| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11186 Z= 0.101 Angle : 0.526 8.555 15098 Z= 0.265 Chirality : 0.042 0.182 1701 Planarity : 0.003 0.040 1923 Dihedral : 6.005 74.801 1504 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.32 % Allowed : 13.81 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1331 helix: 0.10 (0.24), residues: 530 sheet: -0.88 (0.32), residues: 255 loop : -0.55 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 148 HIS 0.002 0.000 HIS B 304 PHE 0.013 0.001 PHE A 660 TYR 0.009 0.001 TYR A 441 ARG 0.006 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 446) hydrogen bonds : angle 4.91421 ( 1275) covalent geometry : bond 0.00235 (11186) covalent geometry : angle 0.52626 (15098) *********************** 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 119 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7879 (mmm) cc_final: 0.7665 (mmm) REVERT: A 84 MET cc_start: 0.6318 (mtp) cc_final: 0.6074 (mtm) REVERT: A 512 PHE cc_start: 0.8238 (t80) cc_final: 0.7893 (t80) REVERT: B 84 MET cc_start: 0.7832 (mtp) cc_final: 0.7602 (mtp) REVERT: B 650 SER cc_start: 0.8920 (m) cc_final: 0.8614 (p) REVERT: C 230 TYR cc_start: 0.8105 (t80) cc_final: 0.7491 (t80) REVERT: C 301 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7567 (p) outliers start: 16 outliers final: 6 residues processed: 117 average time/residue: 0.2038 time to fit residues: 36.1888 Evaluate side-chains 84 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 B residue 58 THR Chi-restraints excluded: chain B residue 641 LEU 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 113 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072084 restraints weight = 34670.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073966 restraints weight = 20202.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075268 restraints weight = 13919.548| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11186 Z= 0.131 Angle : 0.537 7.957 15098 Z= 0.274 Chirality : 0.043 0.148 1701 Planarity : 0.003 0.040 1923 Dihedral : 6.008 75.511 1504 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1331 helix: 0.22 (0.23), residues: 541 sheet: -0.88 (0.32), residues: 253 loop : -0.45 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.001 0.000 HIS B 463 PHE 0.012 0.001 PHE A 660 TYR 0.017 0.001 TYR B 289 ARG 0.005 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 446) hydrogen bonds : angle 4.89888 ( 1275) covalent geometry : bond 0.00312 (11186) covalent geometry : angle 0.53714 (15098) *********************** 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: 21 poor density : 84 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.6304 (mtp) cc_final: 0.6082 (mtm) REVERT: A 586 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 487 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9238 (mm) REVERT: B 650 SER cc_start: 0.8843 (m) cc_final: 0.8557 (p) REVERT: C 301 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7661 (p) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.2235 time to fit residues: 33.5080 Evaluate side-chains 88 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 372 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU 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 B residue 487 LEU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 224 VAL 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 126 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 105 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.083907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073792 restraints weight = 34898.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075731 restraints weight = 20212.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077058 restraints weight = 13794.114| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11186 Z= 0.092 Angle : 0.502 8.626 15098 Z= 0.254 Chirality : 0.042 0.140 1701 Planarity : 0.003 0.039 1923 Dihedral : 5.872 74.373 1504 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.74 % Allowed : 14.06 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1331 helix: 0.36 (0.24), residues: 537 sheet: -0.77 (0.32), residues: 263 loop : -0.32 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.002 0.000 HIS B 304 PHE 0.013 0.001 PHE A 660 TYR 0.019 0.001 TYR B 289 ARG 0.004 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 446) hydrogen bonds : angle 4.66406 ( 1275) covalent geometry : bond 0.00211 (11186) covalent geometry : angle 0.50219 (15098) *********************** 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 112 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.6776 (mmpt) cc_final: 0.6533 (mtmm) REVERT: A 586 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 649 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8576 (t) REVERT: B 650 SER cc_start: 0.8844 (m) cc_final: 0.8584 (p) REVERT: C 230 TYR cc_start: 0.7999 (t80) cc_final: 0.7361 (t80) outliers start: 21 outliers final: 12 residues processed: 108 average time/residue: 0.2761 time to fit residues: 45.4844 Evaluate side-chains 93 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 372 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU 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 B residue 649 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.081912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071511 restraints weight = 35579.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.073430 restraints weight = 20672.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074767 restraints weight = 14190.995| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5574 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= 0.139 Angle : 0.541 9.173 15098 Z= 0.274 Chirality : 0.043 0.152 1701 Planarity : 0.003 0.040 1923 Dihedral : 5.951 76.950 1504 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.90 % Allowed : 14.72 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1331 helix: 0.37 (0.23), residues: 541 sheet: -0.75 (0.33), residues: 253 loop : -0.37 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.002 0.001 HIS A 197 PHE 0.011 0.001 PHE A 660 TYR 0.020 0.001 TYR B 289 ARG 0.003 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 446) hydrogen bonds : angle 4.76374 ( 1275) covalent geometry : bond 0.00327 (11186) covalent geometry : angle 0.54060 (15098) *********************** 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 106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 180 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7266 (p0) REVERT: B 635 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7877 (p) REVERT: B 649 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8554 (t) REVERT: B 650 SER cc_start: 0.8883 (m) cc_final: 0.8599 (p) outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 0.1993 time to fit residues: 31.4142 Evaluate side-chains 93 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU 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 B residue 455 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 670 LEU 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 21 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.083136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073025 restraints weight = 34835.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074933 restraints weight = 20185.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076255 restraints weight = 13869.112| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5645 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= 0.100 Angle : 0.522 9.692 15098 Z= 0.264 Chirality : 0.042 0.187 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.879 76.164 1504 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1331 helix: 0.42 (0.23), residues: 541 sheet: -0.76 (0.32), residues: 266 loop : -0.23 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.001 0.000 HIS B 304 PHE 0.011 0.001 PHE A 6 TYR 0.016 0.001 TYR B 289 ARG 0.004 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 446) hydrogen bonds : angle 4.67091 ( 1275) covalent geometry : bond 0.00229 (11186) covalent geometry : angle 0.52183 (15098) *********************** 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 109 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.7015 (mmpt) cc_final: 0.6758 (mttp) REVERT: A 586 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 589 MET cc_start: 0.9058 (mmt) cc_final: 0.8720 (mmt) REVERT: B 635 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7777 (p) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.2142 time to fit residues: 33.8101 Evaluate side-chains 93 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR 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 B residue 635 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.082236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.071873 restraints weight = 35139.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073754 restraints weight = 20430.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075078 restraints weight = 14122.060| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11186 Z= 0.123 Angle : 0.546 11.066 15098 Z= 0.275 Chirality : 0.043 0.188 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.904 76.785 1504 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.57 % Allowed : 14.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1331 helix: 0.42 (0.24), residues: 541 sheet: -0.72 (0.32), residues: 263 loop : -0.21 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 148 HIS 0.001 0.000 HIS A 426 PHE 0.010 0.001 PHE B 609 TYR 0.023 0.001 TYR B 289 ARG 0.003 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 446) hydrogen bonds : angle 4.68961 ( 1275) covalent geometry : bond 0.00288 (11186) covalent geometry : angle 0.54622 (15098) *********************** 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 103 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.7093 (mmpt) cc_final: 0.6831 (mtmm) REVERT: A 586 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 635 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7865 (p) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.2066 time to fit residues: 30.6288 Evaluate side-chains 94 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 224 VAL 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 19 optimal weight: 0.0870 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 0.1980 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.073801 restraints weight = 34728.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075764 restraints weight = 19761.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077138 restraints weight = 13441.022| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5810 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= 0.092 Angle : 0.543 10.621 15098 Z= 0.267 Chirality : 0.043 0.193 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.789 76.577 1504 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.24 % Allowed : 15.88 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1331 helix: 0.42 (0.24), residues: 539 sheet: -0.68 (0.32), residues: 266 loop : -0.12 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 317 HIS 0.002 0.000 HIS A 304 PHE 0.012 0.001 PHE A 6 TYR 0.023 0.001 TYR B 289 ARG 0.005 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 446) hydrogen bonds : angle 4.62183 ( 1275) covalent geometry : bond 0.00211 (11186) covalent geometry : angle 0.54273 (15098) ********************** 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 101 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 383 LYS cc_start: 0.7197 (mmpt) cc_final: 0.6801 (mtmm) REVERT: A 586 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: B 635 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7774 (p) REVERT: B 649 THR cc_start: 0.8576 (p) cc_final: 0.8264 (t) REVERT: B 650 SER cc_start: 0.8978 (m) cc_final: 0.8454 (t) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.2176 time to fit residues: 31.8066 Evaluate side-chains 95 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain B residue 58 THR 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 B residue 635 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 224 VAL 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 70 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 20 optimal weight: 0.0000 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.084008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073812 restraints weight = 34411.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075732 restraints weight = 19949.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077043 restraints weight = 13672.246| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11186 Z= 0.098 Angle : 0.534 10.283 15098 Z= 0.267 Chirality : 0.043 0.193 1701 Planarity : 0.003 0.041 1923 Dihedral : 5.775 74.912 1504 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 16.05 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1331 helix: 0.44 (0.24), residues: 535 sheet: -0.68 (0.33), residues: 257 loop : -0.11 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 317 HIS 0.001 0.000 HIS A 304 PHE 0.019 0.001 PHE B 63 TYR 0.022 0.001 TYR B 289 ARG 0.003 0.000 ARG A 536 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 446) hydrogen bonds : angle 4.58621 ( 1275) covalent geometry : bond 0.00227 (11186) covalent geometry : angle 0.53406 (15098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.71 seconds wall clock time: 54 minutes 19.40 seconds (3259.40 seconds total)