Starting phenix.real_space_refine on Sat Jul 4 12:12:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.cif" model { file = "/net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7klu_22918/07_2026/7klu_22918.map" } resolution = 3.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1044 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 12466 2.51 5 N 3430 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.61, per 1000 atoms: 0.23 Number of scatterers: 19742 At special positions: 0 Unit cell: (168.062, 131.564, 134.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 88 16.00 P 12 15.00 Mg 4 11.99 O 3738 8.00 N 3430 7.00 C 12466 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: 1.60 Conformation dependent library (CDL) restraints added in 659.4 milliseconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 24 sheets defined 46.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.669A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 135 Processing helix chain 'A' and resid 164 through 173 Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.087A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.557A pdb=" N SER A 207 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.693A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.542A pdb=" N VAL A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.861A pdb=" N VAL A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.505A pdb=" N HIS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 433 removed outlier: 3.538A pdb=" N LYS A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 removed outlier: 3.562A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.530A pdb=" N LYS A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.793A pdb=" N ALA A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.514A pdb=" N ALA A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 550 through 556 removed outlier: 3.984A pdb=" N VAL A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 556 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 588 removed outlier: 4.419A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 4.646A pdb=" N SER A 592 " --> pdb=" O VAL A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 628 removed outlier: 3.934A pdb=" N ARG A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 4.165A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 681 removed outlier: 3.676A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 688 removed outlier: 3.842A pdb=" N ALA A 688 " --> pdb=" O ASP A 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 685 through 688' Processing helix chain 'A' and resid 689 through 701 removed outlier: 3.519A pdb=" N LEU A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.495A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.121A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.705A pdb=" N PHE B 209 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.597A pdb=" N PHE B 264 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 408 through 433 removed outlier: 3.552A pdb=" N LYS B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 454 removed outlier: 5.848A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.590A pdb=" N LYS B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 531 through 540 removed outlier: 3.655A pdb=" N LEU B 537 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.511A pdb=" N ILE B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 590 removed outlier: 3.785A pdb=" N MET B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.655A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET B 624 " --> pdb=" O HIS B 620 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 625 " --> pdb=" O PHE B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 637 removed outlier: 4.054A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.846A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 681 removed outlier: 3.840A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 701 removed outlier: 3.538A pdb=" N VAL B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.757A pdb=" N ASP D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 135 removed outlier: 4.443A pdb=" N ARG D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.510A pdb=" N VAL D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 removed outlier: 4.353A pdb=" N ALA D 182 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 259 through 265 removed outlier: 4.029A pdb=" N LYS D 262 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU D 263 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 264 " --> pdb=" O CYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.659A pdb=" N MET D 300 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.885A pdb=" N TYR D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 433 Processing helix chain 'D' and resid 433 through 444 removed outlier: 3.501A pdb=" N ASP D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 454 removed outlier: 4.127A pdb=" N MET D 448 " --> pdb=" O TYR D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 483 through 489 Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 511 through 517 Processing helix chain 'D' and resid 518 through 520 No H-bonds generated for 'chain 'D' and resid 518 through 520' Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 549 through 557 removed outlier: 3.873A pdb=" N VAL D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 556 " --> pdb=" O THR D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 591 removed outlier: 3.579A pdb=" N TRP D 585 " --> pdb=" O GLU D 581 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 628 removed outlier: 4.183A pdb=" N ARG D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 654 Processing helix chain 'D' and resid 655 through 657 No H-bonds generated for 'chain 'D' and resid 655 through 657' Processing helix chain 'D' and resid 661 through 680 removed outlier: 3.804A pdb=" N LEU D 667 " --> pdb=" O GLY D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 701 removed outlier: 4.463A pdb=" N GLY D 691 " --> pdb=" O ARG D 687 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.593A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 131 removed outlier: 3.568A pdb=" N GLU C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 removed outlier: 3.710A pdb=" N VAL C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 removed outlier: 3.968A pdb=" N ALA C 182 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 261 through 265 removed outlier: 4.017A pdb=" N PHE C 264 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 265 " --> pdb=" O LYS C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 265' Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.577A pdb=" N VAL C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 307 through 319 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.877A pdb=" N VAL C 355 " --> pdb=" O SER C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.531A pdb=" N ARG C 385 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 433 removed outlier: 4.119A pdb=" N ARG C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 416 " --> pdb=" O ARG C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 444 through 454 removed outlier: 4.161A pdb=" N MET C 448 " --> pdb=" O TYR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 466 removed outlier: 3.550A pdb=" N LYS C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 487 Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 511 through 517 Processing helix chain 'C' and resid 518 through 520 No H-bonds generated for 'chain 'C' and resid 518 through 520' Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 550 through 557 Processing helix chain 'C' and resid 575 through 590 removed outlier: 3.935A pdb=" N LEU C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP C 585 " --> pdb=" O GLU C 581 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 4.300A pdb=" N ARG C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 637 removed outlier: 3.831A pdb=" N LEU C 637 " --> pdb=" O GLU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 655 removed outlier: 3.554A pdb=" N ASN C 655 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 680 removed outlier: 3.731A pdb=" N ALA C 665 " --> pdb=" O GLU C 661 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN C 666 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 667 " --> pdb=" O GLY C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 701 removed outlier: 3.728A pdb=" N LYS C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.679A pdb=" N PHE B 239 " --> pdb=" O HIS A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.844A pdb=" N SER B 219 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.395A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.731A pdb=" N THR A 251 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 219 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 228 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.731A pdb=" N THR A 251 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 219 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 228 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 333 removed outlier: 6.451A pdb=" N VAL A 345 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 328 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A 343 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS A 330 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 341 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 332 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 339 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 removed outlier: 4.127A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 499 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 599 removed outlier: 6.573A pdb=" N ASN A 596 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE A 644 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 327 through 333 removed outlier: 3.824A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 345 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 364 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 481 through 482 removed outlier: 5.236A pdb=" N ILE B 497 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 597 through 599 removed outlier: 3.755A pdb=" N THR B 641 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB5, first strand: chain 'D' and resid 80 through 81 removed outlier: 3.591A pdb=" N ALA C 242 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 219 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG C 214 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 250 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 251 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 92 removed outlier: 7.336A pdb=" N GLN D 91 " --> pdb=" O ILE C 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 290 through 291 removed outlier: 7.227A pdb=" N ILE D 143 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG D 214 " --> pdb=" O HIS D 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 233 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 228 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 290 through 291 removed outlier: 7.227A pdb=" N ILE D 143 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG D 214 " --> pdb=" O HIS D 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 233 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 228 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AC1, first strand: chain 'D' and resid 327 through 333 removed outlier: 3.801A pdb=" N TYR D 327 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 345 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 471 through 472 Processing sheet with id=AC3, first strand: chain 'D' and resid 597 through 599 removed outlier: 3.637A pdb=" N ILE D 644 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 327 through 333 removed outlier: 3.813A pdb=" N TYR C 327 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 364 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 481 through 482 removed outlier: 3.820A pdb=" N GLU C 471 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N LEU C 525 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR C 498 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N CYS C 527 " --> pdb=" O TYR C 498 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C 500 " --> pdb=" O CYS C 527 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE C 497 " --> pdb=" O ILE C 548 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 596 through 599 removed outlier: 6.363A pdb=" N ASN C 596 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE C 644 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LYS C 598 " --> pdb=" O ILE C 644 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2538 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: 4.14 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6517 1.34 - 1.46: 4029 1.46 - 1.58: 9360 1.58 - 1.70: 20 1.70 - 1.81: 160 Bond restraints: 20086 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " 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 C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 20081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 26986 3.36 - 6.72: 99 6.72 - 10.08: 13 10.08 - 13.43: 4 13.43 - 16.79: 4 Bond angle restraints: 27106 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.16 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 110.30 16.65 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP D 901 " pdb=" N3B ANP D 901 " pdb=" PG ANP D 901 " ideal model delta sigma weight residual 126.95 110.33 16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 110.41 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1B ANP C 901 " pdb=" PB ANP C 901 " pdb=" O2B ANP C 901 " ideal model delta sigma weight residual 120.08 109.09 10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 27101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10898 17.92 - 35.85: 1085 35.85 - 53.77: 175 53.77 - 71.70: 50 71.70 - 89.62: 42 Dihedral angle restraints: 12250 sinusoidal: 5054 harmonic: 7196 Sorted by residual: dihedral pdb=" CA ASP A 158 " pdb=" CB ASP A 158 " pdb=" CG ASP A 158 " pdb=" OD1 ASP A 158 " ideal model delta sinusoidal sigma weight residual -30.00 -86.73 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 462 " pdb=" CG GLU A 462 " pdb=" CD GLU A 462 " pdb=" OE1 GLU A 462 " ideal model delta sinusoidal sigma weight residual 0.00 89.62 -89.62 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 89.52 -89.52 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 12247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2630 0.056 - 0.111: 395 0.111 - 0.167: 27 0.167 - 0.223: 0 0.223 - 0.278: 4 Chirality restraints: 3056 Sorted by residual: chirality pdb=" C3' ANP C 901 " pdb=" C2' ANP C 901 " pdb=" C4' ANP C 901 " pdb=" O3' ANP C 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP D 901 " pdb=" C2' ANP D 901 " pdb=" C4' ANP D 901 " pdb=" O3' ANP D 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3053 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 223 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO D 224 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 224 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 224 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 302 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 303 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 303 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 303 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 138 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D 139 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 139 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 139 " 0.019 5.00e-02 4.00e+02 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 203 2.63 - 3.26: 19648 3.26 - 3.89: 36423 3.89 - 4.51: 48605 4.51 - 5.14: 77641 Nonbonded interactions: 182520 Sorted by model distance: nonbonded pdb=" O3G ANP B 901 " pdb="MG MG B 902 " model vdw 2.005 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 902 " model vdw 2.014 2.170 nonbonded pdb=" OD1 ASN D 119 " pdb="MG MG D 902 " model vdw 2.054 2.170 nonbonded pdb=" O3G ANP A 901 " pdb="MG MG A 902 " model vdw 2.059 2.170 nonbonded pdb=" O3G ANP D 901 " pdb="MG MG D 902 " model vdw 2.063 2.170 ... (remaining 182515 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 903)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 903)) selection = (chain 'C' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 903)) selection = (chain 'D' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 903)) } 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.360 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.004 0.144 20086 Z= 0.182 Angle : 0.602 16.792 27106 Z= 0.291 Chirality : 0.040 0.278 3056 Planarity : 0.003 0.076 3440 Dihedral : 15.428 89.620 7574 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.73 (0.17), residues: 2420 helix: 0.11 (0.17), residues: 972 sheet: 0.33 (0.29), residues: 358 loop : -1.27 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 491 TYR 0.019 0.001 TYR B 673 PHE 0.020 0.001 PHE A 183 TRP 0.017 0.001 TRP B 585 HIS 0.004 0.000 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (20086) covalent geometry : angle 0.60210 / 0.29 (27106) hydrogen bonds : bond 0.28547 / 19.34 ( 850) hydrogen bonds : angle 8.16299 / 5.58 ( 2538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 ASN cc_start: 0.8123 (m-40) cc_final: 0.7847 (m110) REVERT: A 623 ARG cc_start: 0.6037 (ttp-170) cc_final: 0.5691 (tpt170) REVERT: B 308 GLU cc_start: 0.6335 (tp30) cc_final: 0.6119 (tp30) REVERT: B 352 MET cc_start: 0.2527 (mmm) cc_final: 0.1927 (ptp) REVERT: C 689 MET cc_start: 0.7825 (ppp) cc_final: 0.6753 (ppp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1357 time to fit residues: 37.3605 Evaluate side-chains 143 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 171 ASN A 200 GLN A 310 GLN A 496 ASN B 144 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN D 655 ASN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.107840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086326 restraints weight = 52421.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088194 restraints weight = 43642.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088159 restraints weight = 42949.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.088884 restraints weight = 28378.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089222 restraints weight = 24878.732| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20086 Z= 0.220 Angle : 0.623 8.773 27106 Z= 0.327 Chirality : 0.044 0.176 3056 Planarity : 0.004 0.058 3440 Dihedral : 5.273 60.940 2692 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.89 % Allowed : 7.66 % Favored : 91.46 % 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: -0.89 (0.17), residues: 2420 helix: 0.17 (0.16), residues: 1050 sheet: 0.26 (0.28), residues: 360 loop : -1.71 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 489 TYR 0.018 0.002 TYR C 317 PHE 0.020 0.002 PHE D 621 TRP 0.017 0.002 TRP B 585 HIS 0.008 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (20086) covalent geometry : angle 0.62308 / 0.33 (27106) hydrogen bonds : bond 0.05455 / 3.67 ( 850) hydrogen bonds : angle 5.27751 / 3.62 ( 2538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 TRP cc_start: 0.5855 (t60) cc_final: 0.5650 (t-100) REVERT: B 479 GLN cc_start: 0.6884 (mp10) cc_final: 0.6573 (mp10) REVERT: D 600 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.6891 (p) REVERT: C 292 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7836 (ptp) outliers start: 19 outliers final: 8 residues processed: 157 average time/residue: 0.1264 time to fit residues: 31.5124 Evaluate side-chains 140 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 183 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS B 146 GLN B 288 ASN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085734 restraints weight = 52535.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087878 restraints weight = 42230.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.088104 restraints weight = 36387.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088365 restraints weight = 27203.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088533 restraints weight = 25164.914| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20086 Z= 0.175 Angle : 0.562 6.570 27106 Z= 0.294 Chirality : 0.042 0.160 3056 Planarity : 0.004 0.046 3440 Dihedral : 5.236 61.764 2692 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.07 % Allowed : 12.14 % Favored : 86.79 % 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: -0.89 (0.17), residues: 2420 helix: 0.25 (0.17), residues: 1036 sheet: 0.23 (0.28), residues: 360 loop : -1.78 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 388 TYR 0.015 0.001 TYR C 317 PHE 0.019 0.001 PHE A 183 TRP 0.014 0.002 TRP B 585 HIS 0.006 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (20086) covalent geometry : angle 0.56249 / 0.29 (27106) hydrogen bonds : bond 0.04782 / 3.22 ( 850) hydrogen bonds : angle 4.90675 / 3.38 ( 2538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 689 MET cc_start: 0.6553 (ptm) cc_final: 0.6292 (ttp) REVERT: B 309 TRP cc_start: 0.5876 (t60) cc_final: 0.5640 (t-100) REVERT: B 432 LYS cc_start: 0.8541 (mptt) cc_final: 0.8231 (mmtm) REVERT: B 677 MET cc_start: 0.8172 (tpp) cc_final: 0.7530 (tpp) REVERT: D 600 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.6721 (p) outliers start: 23 outliers final: 12 residues processed: 161 average time/residue: 0.1214 time to fit residues: 30.8862 Evaluate side-chains 150 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 609 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 37 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086019 restraints weight = 52344.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.087210 restraints weight = 40121.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087926 restraints weight = 30240.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088285 restraints weight = 25574.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088563 restraints weight = 24240.304| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20086 Z= 0.132 Angle : 0.517 8.196 27106 Z= 0.270 Chirality : 0.041 0.159 3056 Planarity : 0.003 0.039 3440 Dihedral : 5.011 61.277 2692 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.21 % Allowed : 14.33 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2420 helix: 0.46 (0.17), residues: 1020 sheet: 0.32 (0.28), residues: 360 loop : -1.67 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 388 TYR 0.014 0.001 TYR C 317 PHE 0.018 0.001 PHE A 183 TRP 0.012 0.001 TRP C 231 HIS 0.005 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (20086) covalent geometry : angle 0.51706 / 0.27 (27106) hydrogen bonds : bond 0.03969 / 2.67 ( 850) hydrogen bonds : angle 4.62309 / 3.19 ( 2538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8196 (m-80) cc_final: 0.7979 (m-80) REVERT: B 309 TRP cc_start: 0.5967 (t60) cc_final: 0.5755 (t-100) REVERT: B 344 TYR cc_start: 0.7739 (m-80) cc_final: 0.7347 (m-80) REVERT: D 600 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6491 (p) REVERT: D 622 LEU cc_start: 0.7521 (mm) cc_final: 0.7141 (mm) REVERT: C 292 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8056 (ptp) outliers start: 26 outliers final: 13 residues processed: 166 average time/residue: 0.1225 time to fit residues: 32.3905 Evaluate side-chains 151 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 68 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 530 GLN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 496 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.105339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.083423 restraints weight = 52278.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084478 restraints weight = 40916.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085237 restraints weight = 30921.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085843 restraints weight = 25993.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086154 restraints weight = 24172.022| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20086 Z= 0.249 Angle : 0.633 7.423 27106 Z= 0.330 Chirality : 0.045 0.157 3056 Planarity : 0.004 0.043 3440 Dihedral : 5.553 63.318 2692 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.82 % Allowed : 15.92 % Favored : 82.26 % 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: -1.11 (0.17), residues: 2420 helix: 0.10 (0.16), residues: 1036 sheet: 0.04 (0.28), residues: 364 loop : -1.91 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 368 TYR 0.015 0.002 TYR C 317 PHE 0.019 0.002 PHE A 183 TRP 0.017 0.002 TRP C 231 HIS 0.006 0.001 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (20086) covalent geometry : angle 0.63340 / 0.33 (27106) hydrogen bonds : bond 0.04950 / 3.36 ( 850) hydrogen bonds : angle 4.88606 / 3.37 ( 2538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: D 551 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: D 600 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6476 (p) REVERT: C 666 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7176 (tm-30) outliers start: 39 outliers final: 24 residues processed: 165 average time/residue: 0.1278 time to fit residues: 33.7192 Evaluate side-chains 157 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 609 MET Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 103 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 0.0010 chunk 82 optimal weight: 10.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 GLN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.107434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085542 restraints weight = 51959.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086613 restraints weight = 39839.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.087448 restraints weight = 30146.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.088008 restraints weight = 25117.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088300 restraints weight = 23930.863| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20086 Z= 0.123 Angle : 0.519 8.595 27106 Z= 0.270 Chirality : 0.041 0.158 3056 Planarity : 0.003 0.039 3440 Dihedral : 5.043 62.063 2692 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.82 % Allowed : 17.09 % Favored : 81.09 % 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: -0.73 (0.17), residues: 2420 helix: 0.51 (0.17), residues: 1028 sheet: 0.21 (0.28), residues: 360 loop : -1.78 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 388 TYR 0.013 0.001 TYR C 317 PHE 0.020 0.001 PHE A 183 TRP 0.012 0.002 TRP C 231 HIS 0.004 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (20086) covalent geometry : angle 0.51893 / 0.27 (27106) hydrogen bonds : bond 0.03736 / 2.51 ( 850) hydrogen bonds : angle 4.52124 / 3.12 ( 2538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 344 TYR cc_start: 0.7730 (m-80) cc_final: 0.7365 (m-80) REVERT: D 600 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6325 (p) REVERT: C 292 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7941 (ptp) REVERT: C 661 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: C 666 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7085 (tm-30) outliers start: 39 outliers final: 23 residues processed: 179 average time/residue: 0.1291 time to fit residues: 36.4768 Evaluate side-chains 166 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 205 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 639 GLN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084237 restraints weight = 52522.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085583 restraints weight = 40634.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086274 restraints weight = 29833.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086542 restraints weight = 25647.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086814 restraints weight = 24450.506| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20086 Z= 0.191 Angle : 0.581 9.524 27106 Z= 0.301 Chirality : 0.043 0.199 3056 Planarity : 0.003 0.037 3440 Dihedral : 5.269 61.624 2692 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.96 % Allowed : 17.83 % Favored : 80.21 % 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: -0.94 (0.17), residues: 2420 helix: 0.36 (0.17), residues: 1032 sheet: 0.11 (0.28), residues: 364 loop : -1.94 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 388 TYR 0.014 0.001 TYR C 317 PHE 0.020 0.001 PHE A 183 TRP 0.015 0.002 TRP C 231 HIS 0.005 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (20086) covalent geometry : angle 0.58068 / 0.30 (27106) hydrogen bonds : bond 0.04311 / 2.92 ( 850) hydrogen bonds : angle 4.63608 / 3.20 ( 2538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.779 Fit side-chains REVERT: A 581 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: A 639 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: D 600 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6369 (p) REVERT: D 622 LEU cc_start: 0.7597 (mm) cc_final: 0.7275 (mm) REVERT: C 661 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: C 666 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7195 (tm-30) outliers start: 42 outliers final: 26 residues processed: 176 average time/residue: 0.1235 time to fit residues: 35.0298 Evaluate side-chains 163 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 114 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN C 496 ASN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.107863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086082 restraints weight = 51905.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088167 restraints weight = 39959.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.088234 restraints weight = 36976.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088615 restraints weight = 25816.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089118 restraints weight = 23721.643| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20086 Z= 0.109 Angle : 0.520 10.113 27106 Z= 0.267 Chirality : 0.041 0.179 3056 Planarity : 0.003 0.039 3440 Dihedral : 4.891 59.764 2692 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2420 helix: 0.65 (0.17), residues: 1030 sheet: 0.32 (0.29), residues: 360 loop : -1.76 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 388 TYR 0.012 0.001 TYR C 317 PHE 0.021 0.001 PHE A 183 TRP 0.023 0.002 TRP A 585 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20086) covalent geometry : angle 0.51978 / 0.27 (27106) hydrogen bonds : bond 0.03450 / 2.31 ( 850) hydrogen bonds : angle 4.38758 / 3.03 ( 2538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 141 MET cc_start: 0.7377 (ptp) cc_final: 0.7130 (mtp) REVERT: B 71 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5363 (mp) REVERT: B 344 TYR cc_start: 0.7711 (m-80) cc_final: 0.7371 (m-80) REVERT: D 600 THR cc_start: 0.6980 (OUTLIER) cc_final: 0.6189 (p) REVERT: D 622 LEU cc_start: 0.7557 (mm) cc_final: 0.7196 (mm) REVERT: C 292 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8050 (ptp) REVERT: C 587 ARG cc_start: 0.7146 (mmm-85) cc_final: 0.6735 (mtt-85) REVERT: C 661 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5868 (mp0) REVERT: C 666 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7116 (tm-30) outliers start: 37 outliers final: 23 residues processed: 175 average time/residue: 0.1220 time to fit residues: 34.1813 Evaluate side-chains 166 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 38 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 216 optimal weight: 0.0980 chunk 221 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 639 GLN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.105887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083745 restraints weight = 52197.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084579 restraints weight = 38785.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084966 restraints weight = 34806.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086313 restraints weight = 27888.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086350 restraints weight = 23033.393| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20086 Z= 0.203 Angle : 0.597 10.718 27106 Z= 0.307 Chirality : 0.043 0.177 3056 Planarity : 0.004 0.037 3440 Dihedral : 5.219 60.202 2692 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.73 % Allowed : 18.35 % Favored : 79.93 % 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: -0.84 (0.17), residues: 2420 helix: 0.47 (0.17), residues: 1020 sheet: 0.18 (0.29), residues: 364 loop : -1.90 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 495 TYR 0.019 0.002 TYR C 498 PHE 0.021 0.001 PHE A 183 TRP 0.020 0.002 TRP A 585 HIS 0.005 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (20086) covalent geometry : angle 0.59731 / 0.31 (27106) hydrogen bonds : bond 0.04295 / 2.91 ( 850) hydrogen bonds : angle 4.56969 / 3.16 ( 2538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 581 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: B 71 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5463 (mp) REVERT: D 583 MET cc_start: 0.6659 (tpt) cc_final: 0.6281 (tpt) REVERT: D 600 THR cc_start: 0.6966 (OUTLIER) cc_final: 0.6151 (p) REVERT: C 587 ARG cc_start: 0.7255 (mmm-85) cc_final: 0.6711 (mtt-85) REVERT: C 661 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: C 666 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7230 (tm-30) outliers start: 37 outliers final: 23 residues processed: 166 average time/residue: 0.1254 time to fit residues: 33.9456 Evaluate side-chains 159 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084223 restraints weight = 52066.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085948 restraints weight = 38197.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085986 restraints weight = 35498.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086214 restraints weight = 26305.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086743 restraints weight = 24397.344| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20086 Z= 0.159 Angle : 0.568 11.210 27106 Z= 0.291 Chirality : 0.042 0.175 3056 Planarity : 0.003 0.063 3440 Dihedral : 5.117 60.198 2692 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.59 % Allowed : 18.63 % Favored : 79.79 % 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: -0.78 (0.17), residues: 2420 helix: 0.51 (0.17), residues: 1020 sheet: 0.21 (0.29), residues: 364 loop : -1.86 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.015 0.001 TYR A 229 PHE 0.022 0.001 PHE A 183 TRP 0.022 0.002 TRP A 585 HIS 0.005 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (20086) covalent geometry : angle 0.56782 / 0.29 (27106) hydrogen bonds : bond 0.03934 / 2.66 ( 850) hydrogen bonds : angle 4.49348 / 3.11 ( 2538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 141 MET cc_start: 0.7411 (ptp) cc_final: 0.7174 (mtp) REVERT: A 581 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: B 71 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5437 (mp) REVERT: B 344 TYR cc_start: 0.7753 (m-80) cc_final: 0.7336 (m-80) REVERT: B 352 MET cc_start: 0.3559 (mmm) cc_final: 0.2214 (ptp) REVERT: D 337 LEU cc_start: 0.7899 (pp) cc_final: 0.7655 (pt) REVERT: D 583 MET cc_start: 0.6663 (tpt) cc_final: 0.6329 (tpt) REVERT: D 600 THR cc_start: 0.7091 (OUTLIER) cc_final: 0.6240 (p) REVERT: C 587 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.6796 (mtt-85) REVERT: C 661 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: C 666 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7228 (tm-30) outliers start: 34 outliers final: 27 residues processed: 165 average time/residue: 0.1274 time to fit residues: 34.2342 Evaluate side-chains 164 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 158 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 152 optimal weight: 0.0570 chunk 111 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 216 optimal weight: 0.2980 overall best weight: 2.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 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 = 0.3764 r_free = 0.3764 target = 0.106569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084404 restraints weight = 52130.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086104 restraints weight = 38836.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086284 restraints weight = 35500.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086614 restraints weight = 26044.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086859 restraints weight = 23778.302| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 20086 Z= 0.187 Angle : 0.741 59.182 27106 Z= 0.418 Chirality : 0.045 0.942 3056 Planarity : 0.003 0.061 3440 Dihedral : 5.168 60.225 2692 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.68 % Allowed : 18.63 % Favored : 79.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.78 (0.17), residues: 2420 helix: 0.52 (0.17), residues: 1020 sheet: 0.18 (0.29), residues: 364 loop : -1.86 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.014 0.001 TYR C 317 PHE 0.021 0.001 PHE A 183 TRP 0.021 0.002 TRP A 585 HIS 0.005 0.001 HIS C 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (20086) covalent geometry : angle 0.74084 / 0.42 (27106) hydrogen bonds : bond 0.03915 / 2.64 ( 850) hydrogen bonds : angle 4.49329 / 3.11 ( 2538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.21 seconds wall clock time: 46 minutes 33.68 seconds (2793.68 seconds total)