Starting phenix.real_space_refine on Sun Sep 13 22:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nr2_0487/09_2026/6nr2_0487_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nr2_0487/09_2026/6nr2_0487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nr2_0487/09_2026/6nr2_0487_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nr2_0487/09_2026/6nr2_0487_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nr2_0487/09_2026/6nr2_0487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nr2_0487/09_2026/6nr2_0487.map" } resolution = 4.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 124 5.16 5 C 16944 2.51 5 N 4264 2.21 5 O 4444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25788 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6273 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 21, 'TRANS': 813} Chain breaks: 13 Unresolved non-hydrogen bonds: 590 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 463 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'UNK:plan-1': 21, 'TYR:plan': 1, 'ARG:plan': 11, 'ASP:plan': 20, 'GLU:plan': 32, 'GLN:plan1': 2, 'HIS:plan': 5, 'ASN:plan1': 8, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 348 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'KXP': 1, 'KXS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'KXP:plan-2': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 18 Restraints were copied for chains: B, C, D Time building chain proxies: 7.52, per 1000 atoms: 0.29 Number of scatterers: 25788 At special positions: 0 Unit cell: (152.28, 152.28, 144.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 12 15.00 O 4444 8.00 N 4264 7.00 C 16944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS D 648 " - pdb=" SG CYS D1042 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 930.7 milliseconds 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 4 sheets defined 77.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 187 through 203 Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.675A pdb=" N VAL A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.892A pdb=" N LEU A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.983A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.665A pdb=" N GLU A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.561A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.855A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.710A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 480 removed outlier: 4.381A pdb=" N PHE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.772A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.623A pdb=" N ASN A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 removed outlier: 4.016A pdb=" N ARG A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.684A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.511A pdb=" N SER A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 586 through 603 removed outlier: 3.698A pdb=" N SER A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.730A pdb=" N ALA A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 655 through 664 removed outlier: 3.777A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 removed outlier: 3.712A pdb=" N GLN A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 702 through 708 removed outlier: 4.125A pdb=" N GLY A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 732 Processing helix chain 'A' and resid 733 through 758 removed outlier: 3.524A pdb=" N VAL A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 790 through 795 removed outlier: 3.975A pdb=" N PHE A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.618A pdb=" N VAL A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 850 removed outlier: 4.353A pdb=" N SER A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 889 removed outlier: 4.218A pdb=" N ARG A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 912 removed outlier: 3.560A pdb=" N PHE A 899 " --> pdb=" O TRP A 895 " (cutoff:3.500A) Proline residue: A 906 - end of helix Processing helix chain 'A' and resid 954 through 978 removed outlier: 3.600A pdb=" N MET A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 972 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1006 removed outlier: 3.680A pdb=" N SER A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1013 No H-bonds generated for 'chain 'A' and resid 1011 through 1013' Processing helix chain 'A' and resid 1014 through 1026 removed outlier: 3.909A pdb=" N ALA A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A1024 " --> pdb=" O ILE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1068 removed outlier: 3.646A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A1065 " --> pdb=" O ASN A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1100 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 187 through 203 Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.676A pdb=" N VAL B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.892A pdb=" N LEU B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 3.984A pdb=" N ILE B 366 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 385 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.666A pdb=" N GLU B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 3.562A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.854A pdb=" N ALA B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 468 removed outlier: 3.711A pdb=" N LEU B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 480 removed outlier: 4.381A pdb=" N PHE B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.772A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.622A pdb=" N ASN B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 533 removed outlier: 4.015A pdb=" N ARG B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.683A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.511A pdb=" N SER B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.697A pdb=" N SER B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.729A pdb=" N ALA B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 655 through 664 removed outlier: 3.777A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 removed outlier: 3.712A pdb=" N GLN B 675 " --> pdb=" O GLN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 702 through 708 removed outlier: 4.126A pdb=" N GLY B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 732 Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.524A pdb=" N VAL B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 790 through 795 removed outlier: 3.975A pdb=" N PHE B 794 " --> pdb=" O GLY B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 818 removed outlier: 3.619A pdb=" N VAL B 814 " --> pdb=" O ILE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 850 removed outlier: 4.354A pdb=" N SER B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 889 removed outlier: 4.217A pdb=" N ARG B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 912 removed outlier: 3.559A pdb=" N PHE B 899 " --> pdb=" O TRP B 895 " (cutoff:3.500A) Proline residue: B 906 - end of helix Processing helix chain 'B' and resid 954 through 978 removed outlier: 3.601A pdb=" N MET B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN B 972 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1006 removed outlier: 3.680A pdb=" N SER B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1013 No H-bonds generated for 'chain 'B' and resid 1011 through 1013' Processing helix chain 'B' and resid 1014 through 1026 removed outlier: 3.909A pdb=" N ALA B1018 " --> pdb=" O PHE B1014 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B1024 " --> pdb=" O ILE B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1068 removed outlier: 3.646A pdb=" N ALA B1053 " --> pdb=" O ASN B1049 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP B1054 " --> pdb=" O GLU B1050 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B1065 " --> pdb=" O ASN B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1100 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 187 through 203 Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 310 through 322 Processing helix chain 'C' and resid 334 through 343 removed outlier: 3.675A pdb=" N VAL C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.891A pdb=" N LEU C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 3.982A pdb=" N ILE C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.665A pdb=" N GLU C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.562A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.854A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 468 removed outlier: 3.710A pdb=" N LEU C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 480 removed outlier: 4.381A pdb=" N PHE C 477 " --> pdb=" O PHE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 500 removed outlier: 3.773A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.622A pdb=" N ASN C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 533 removed outlier: 4.016A pdb=" N ARG C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.683A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 581 removed outlier: 3.511A pdb=" N SER C 577 " --> pdb=" O LYS C 573 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 584 No H-bonds generated for 'chain 'C' and resid 582 through 584' Processing helix chain 'C' and resid 586 through 603 removed outlier: 3.698A pdb=" N SER C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.729A pdb=" N ALA C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 645 Processing helix chain 'C' and resid 655 through 664 removed outlier: 3.777A pdb=" N VAL C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.711A pdb=" N GLN C 675 " --> pdb=" O GLN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 702 through 708 removed outlier: 4.126A pdb=" N GLY C 706 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 732 Processing helix chain 'C' and resid 733 through 758 removed outlier: 3.524A pdb=" N VAL C 737 " --> pdb=" O SER C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 790 through 795 removed outlier: 3.975A pdb=" N PHE C 794 " --> pdb=" O GLY C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 818 removed outlier: 3.618A pdb=" N VAL C 814 " --> pdb=" O ILE C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 850 removed outlier: 4.352A pdb=" N SER C 826 " --> pdb=" O SER C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 889 removed outlier: 4.217A pdb=" N ARG C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 912 removed outlier: 3.559A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Proline residue: C 906 - end of helix Processing helix chain 'C' and resid 954 through 978 removed outlier: 3.600A pdb=" N MET C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN C 972 " --> pdb=" O ILE C 968 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1006 removed outlier: 3.679A pdb=" N SER C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1011 through 1013 No H-bonds generated for 'chain 'C' and resid 1011 through 1013' Processing helix chain 'C' and resid 1014 through 1026 removed outlier: 3.910A pdb=" N ALA C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET C1024 " --> pdb=" O ILE C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1068 removed outlier: 3.645A pdb=" N ALA C1053 " --> pdb=" O ASN C1049 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP C1054 " --> pdb=" O GLU C1050 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C1065 " --> pdb=" O ASN C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1100 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 277 through 287 Processing helix chain 'D' and resid 310 through 322 Processing helix chain 'D' and resid 334 through 343 removed outlier: 3.675A pdb=" N VAL D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.892A pdb=" N LEU D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.983A pdb=" N ILE D 366 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG D 368 " --> pdb=" O ARG D 364 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 385 Processing helix chain 'D' and resid 403 through 420 removed outlier: 3.665A pdb=" N GLU D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 436 removed outlier: 3.561A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.855A pdb=" N ALA D 442 " --> pdb=" O GLN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 468 removed outlier: 3.711A pdb=" N LEU D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 480 removed outlier: 4.382A pdb=" N PHE D 477 " --> pdb=" O PHE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.773A pdb=" N ASN D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 516 removed outlier: 3.623A pdb=" N ASN D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 533 removed outlier: 4.016A pdb=" N ARG D 533 " --> pdb=" O GLU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.684A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.511A pdb=" N SER D 577 " --> pdb=" O LYS D 573 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 584 No H-bonds generated for 'chain 'D' and resid 582 through 584' Processing helix chain 'D' and resid 586 through 603 removed outlier: 3.698A pdb=" N SER D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.730A pdb=" N ALA D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 655 through 664 removed outlier: 3.778A pdb=" N VAL D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 removed outlier: 3.712A pdb=" N GLN D 675 " --> pdb=" O GLN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 702 through 708 removed outlier: 4.126A pdb=" N GLY D 706 " --> pdb=" O PHE D 702 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 732 Processing helix chain 'D' and resid 733 through 758 removed outlier: 3.525A pdb=" N VAL D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 790 through 795 removed outlier: 3.975A pdb=" N PHE D 794 " --> pdb=" O GLY D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 818 removed outlier: 3.619A pdb=" N VAL D 814 " --> pdb=" O ILE D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 850 removed outlier: 4.353A pdb=" N SER D 826 " --> pdb=" O SER D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 889 removed outlier: 4.218A pdb=" N ARG D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 912 removed outlier: 3.560A pdb=" N PHE D 899 " --> pdb=" O TRP D 895 " (cutoff:3.500A) Proline residue: D 906 - end of helix Processing helix chain 'D' and resid 954 through 978 removed outlier: 3.601A pdb=" N MET D 963 " --> pdb=" O VAL D 959 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN D 972 " --> pdb=" O ILE D 968 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE D 978 " --> pdb=" O LEU D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1006 removed outlier: 3.680A pdb=" N SER D1006 " --> pdb=" O GLN D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1011 through 1013 No H-bonds generated for 'chain 'D' and resid 1011 through 1013' Processing helix chain 'D' and resid 1014 through 1026 removed outlier: 3.909A pdb=" N ALA D1018 " --> pdb=" O PHE D1014 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET D1024 " --> pdb=" O ILE D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1068 removed outlier: 3.646A pdb=" N ALA D1053 " --> pdb=" O ASN D1049 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS D1065 " --> pdb=" O ASN D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1100 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 211 removed outlier: 6.241A pdb=" N ALA A 177 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL A 210 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.242A pdb=" N ALA B 177 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 210 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 179 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 211 removed outlier: 6.242A pdb=" N ALA C 177 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL C 210 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE C 179 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 211 removed outlier: 6.241A pdb=" N ALA D 177 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL D 210 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE D 179 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) 1708 hydrogen bonds defined for protein. 5124 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: 4.42 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3956 1.31 - 1.44: 7544 1.44 - 1.56: 14664 1.56 - 1.69: 16 1.69 - 1.81: 184 Bond restraints: 26364 Sorted by residual: bond pdb=" C08 KXS C1302 " pdb=" N10 KXS C1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C08 KXS B1302 " pdb=" N10 KXS B1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C08 KXS A1302 " pdb=" N10 KXS A1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C08 KXS D1302 " pdb=" N10 KXS D1302 " ideal model delta sigma weight residual 1.355 1.446 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" O41 KXP B1301 " pdb=" P42 KXP B1301 " ideal model delta sigma weight residual 1.725 1.649 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 26359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 35477 3.69 - 7.38: 447 7.38 - 11.08: 28 11.08 - 14.77: 0 14.77 - 18.46: 4 Bond angle restraints: 35956 Sorted by residual: angle pdb=" C GLN B 761 " pdb=" N LYS B 762 " pdb=" CA LYS B 762 " ideal model delta sigma weight residual 120.82 131.08 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C GLN C 761 " pdb=" N LYS C 762 " pdb=" CA LYS C 762 " ideal model delta sigma weight residual 120.82 131.07 -10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" C GLN D 761 " pdb=" N LYS D 762 " pdb=" CA LYS D 762 " ideal model delta sigma weight residual 120.82 131.05 -10.23 1.50e+00 4.44e-01 4.65e+01 angle pdb=" C GLN A 761 " pdb=" N LYS A 762 " pdb=" CA LYS A 762 " ideal model delta sigma weight residual 120.82 131.05 -10.23 1.50e+00 4.44e-01 4.65e+01 angle pdb=" O24 KXP A1301 " pdb=" P25 KXP A1301 " pdb=" O28 KXP A1301 " ideal model delta sigma weight residual 90.95 109.41 -18.46 3.00e+00 1.11e-01 3.79e+01 ... (remaining 35951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 15280 34.20 - 68.39: 140 68.39 - 102.59: 20 102.59 - 136.79: 0 136.79 - 170.98: 4 Dihedral angle restraints: 15444 sinusoidal: 5312 harmonic: 10132 Sorted by residual: dihedral pdb=" CA MET A 858 " pdb=" C MET A 858 " pdb=" N LEU A 859 " pdb=" CA LEU A 859 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA MET C 858 " pdb=" C MET C 858 " pdb=" N LEU C 859 " pdb=" CA LEU C 859 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA MET D 858 " pdb=" C MET D 858 " pdb=" N LEU D 859 " pdb=" CA LEU D 859 " ideal model delta harmonic sigma weight residual -180.00 -152.26 -27.74 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 15441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3438 0.060 - 0.121: 703 0.121 - 0.181: 94 0.181 - 0.242: 17 0.242 - 0.302: 4 Chirality restraints: 4256 Sorted by residual: chirality pdb=" CA PHE D 447 " pdb=" N PHE D 447 " pdb=" C PHE D 447 " pdb=" CB PHE D 447 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PHE C 447 " pdb=" N PHE C 447 " pdb=" C PHE C 447 " pdb=" CB PHE C 447 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PHE B 447 " pdb=" N PHE B 447 " pdb=" C PHE B 447 " pdb=" CB PHE B 447 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4253 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 864 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ILE A 864 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 864 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 865 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 864 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C ILE D 864 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE D 864 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP D 865 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 864 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C ILE C 864 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE C 864 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP C 865 " 0.017 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 6354 2.78 - 3.31: 24327 3.31 - 3.84: 40025 3.84 - 4.37: 42457 4.37 - 4.90: 73816 Nonbonded interactions: 186979 Sorted by model distance: nonbonded pdb=" OE1 GLU B 782 " pdb=" OH TYR B 793 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU D 782 " pdb=" OH TYR D 793 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU A 782 " pdb=" OH TYR A 793 " model vdw 2.256 3.040 nonbonded pdb=" OE1 GLU C 782 " pdb=" OH TYR C 793 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 687 " pdb=" OG SER B 711 " model vdw 2.277 3.040 ... (remaining 186974 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.860 Find NCS groups from input model: 0.250 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.007 0.091 26368 Z= 0.333 Angle : 1.047 18.459 35964 Z= 0.589 Chirality : 0.050 0.302 4256 Planarity : 0.008 0.055 4416 Dihedral : 11.502 170.983 8800 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.17 % Allowed : 3.76 % Favored : 96.07 % 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: -2.86 (0.12), residues: 3160 helix: -1.40 (0.09), residues: 2220 sheet: 0.43 (0.43), residues: 140 loop : -3.36 (0.16), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 688 TYR 0.037 0.003 TYR B 772 PHE 0.038 0.003 PHE A 867 TRP 0.030 0.003 TRP B 876 HIS 0.006 0.002 HIS B 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00705 / 0.33 (26364) covalent geometry : angle 1.04663 / 0.59 (35956) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 2.73030 / 1.37 ( 8) hydrogen bonds : bond 0.17161 / 11.67 ( 1708) hydrogen bonds : angle 6.36816 / 4.48 ( 5124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 677 time to evaluate : 0.981 Fit side-chains REVERT: A 744 PHE cc_start: 0.8010 (t80) cc_final: 0.7708 (t80) REVERT: A 761 GLN cc_start: 0.8687 (tt0) cc_final: 0.8216 (pp30) REVERT: A 877 MET cc_start: 0.9115 (tpp) cc_final: 0.8855 (mmm) REVERT: A 895 TRP cc_start: 0.7280 (t-100) cc_final: 0.6958 (t60) REVERT: A 904 TYR cc_start: 0.6901 (p90) cc_final: 0.6655 (p90) REVERT: A 905 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 1048 ASP cc_start: 0.8821 (m-30) cc_final: 0.8560 (m-30) REVERT: B 744 PHE cc_start: 0.8135 (t80) cc_final: 0.7821 (t80) REVERT: B 761 GLN cc_start: 0.8667 (tt0) cc_final: 0.8230 (pp30) REVERT: B 895 TRP cc_start: 0.7170 (t-100) cc_final: 0.6926 (t60) REVERT: B 904 TYR cc_start: 0.6729 (p90) cc_final: 0.6523 (p90) REVERT: B 905 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 1046 ASN cc_start: 0.7744 (t0) cc_final: 0.7542 (t0) REVERT: B 1048 ASP cc_start: 0.8844 (m-30) cc_final: 0.8589 (m-30) REVERT: C 744 PHE cc_start: 0.8131 (t80) cc_final: 0.7822 (t80) REVERT: C 761 GLN cc_start: 0.8665 (tt0) cc_final: 0.8208 (pp30) REVERT: C 877 MET cc_start: 0.9091 (tpp) cc_final: 0.8842 (mmm) REVERT: C 895 TRP cc_start: 0.7185 (t-100) cc_final: 0.6945 (t60) REVERT: C 905 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7675 (mt-10) REVERT: C 1046 ASN cc_start: 0.7742 (t0) cc_final: 0.7542 (t0) REVERT: C 1048 ASP cc_start: 0.8843 (m-30) cc_final: 0.8588 (m-30) REVERT: D 744 PHE cc_start: 0.8144 (t80) cc_final: 0.7831 (t80) REVERT: D 761 GLN cc_start: 0.8664 (tt0) cc_final: 0.8202 (pp30) REVERT: D 877 MET cc_start: 0.9068 (tpp) cc_final: 0.8832 (mmm) REVERT: D 895 TRP cc_start: 0.7191 (t-100) cc_final: 0.6946 (t60) REVERT: D 905 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7539 (mt-10) REVERT: D 1046 ASN cc_start: 0.7748 (t0) cc_final: 0.7542 (t0) REVERT: D 1048 ASP cc_start: 0.8846 (m-30) cc_final: 0.8591 (m-30) outliers start: 4 outliers final: 4 residues processed: 681 average time/residue: 0.1450 time to fit residues: 163.6097 Evaluate side-chains 332 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 328 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain D residue 453 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 256 ASN A 419 ASN A 480 ASN A 500 ASN A 572 ASN B 173 GLN B 256 ASN B 419 ASN B 480 ASN B 500 ASN B 572 ASN C 173 GLN C 256 ASN C 419 ASN C 480 ASN C 500 ASN C 572 ASN D 173 GLN D 256 ASN D 419 ASN D 480 ASN D 500 ASN D 572 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086276 restraints weight = 62875.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088648 restraints weight = 35926.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090156 restraints weight = 25472.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091151 restraints weight = 20558.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091690 restraints weight = 17984.368| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26368 Z= 0.184 Angle : 0.640 7.138 35964 Z= 0.331 Chirality : 0.039 0.180 4256 Planarity : 0.004 0.035 4416 Dihedral : 10.248 127.905 3924 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.32 % Allowed : 10.98 % Favored : 84.70 % 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: -0.46 (0.14), residues: 3160 helix: 0.48 (0.10), residues: 2284 sheet: 0.77 (0.44), residues: 140 loop : -2.95 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 828 TYR 0.020 0.002 TYR D 904 PHE 0.025 0.002 PHE B 709 TRP 0.020 0.002 TRP D 876 HIS 0.005 0.002 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (26364) covalent geometry : angle 0.63909 / 0.33 (35956) SS BOND : bond 0.00038 / 0.02 ( 4) SS BOND : angle 2.05484 / 1.02 ( 8) hydrogen bonds : bond 0.05575 / 3.88 ( 1708) hydrogen bonds : angle 4.24106 / 3.01 ( 5124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 357 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7006 (mmm) cc_final: 0.5586 (mmm) REVERT: A 480 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8140 (t0) REVERT: A 641 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8172 (mm-30) REVERT: A 662 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 667 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7884 (tm-30) REVERT: A 1003 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 1048 ASP cc_start: 0.8651 (m-30) cc_final: 0.8436 (m-30) REVERT: A 1058 MET cc_start: 0.9140 (mmm) cc_final: 0.8359 (mmt) REVERT: B 161 MET cc_start: 0.6987 (mmm) cc_final: 0.5562 (mmm) REVERT: B 480 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8110 (t0) REVERT: B 662 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7879 (mm-30) REVERT: B 667 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 1003 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 1048 ASP cc_start: 0.8662 (m-30) cc_final: 0.8461 (m-30) REVERT: B 1058 MET cc_start: 0.9145 (mmm) cc_final: 0.8368 (mmt) REVERT: C 161 MET cc_start: 0.6993 (mmm) cc_final: 0.5562 (mmm) REVERT: C 480 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8101 (t0) REVERT: C 662 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7875 (mm-30) REVERT: C 667 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 750 LEU cc_start: 0.9505 (mt) cc_final: 0.9276 (mm) REVERT: C 1003 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8354 (tm-30) REVERT: C 1058 MET cc_start: 0.9147 (mmm) cc_final: 0.8367 (mmt) REVERT: D 161 MET cc_start: 0.7015 (mmm) cc_final: 0.5612 (mmm) REVERT: D 480 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7789 (t0) REVERT: D 527 MET cc_start: 0.8970 (tmm) cc_final: 0.8700 (ttp) REVERT: D 641 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8152 (mm-30) REVERT: D 662 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7861 (mm-30) REVERT: D 667 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7896 (tm-30) REVERT: D 902 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (p) REVERT: D 1003 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 1048 ASP cc_start: 0.8666 (m-30) cc_final: 0.8465 (m-30) REVERT: D 1058 MET cc_start: 0.9139 (mmm) cc_final: 0.8368 (mmt) outliers start: 101 outliers final: 57 residues processed: 425 average time/residue: 0.1378 time to fit residues: 99.4488 Evaluate side-chains 373 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 311 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 760 PHE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 480 ASN Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 756 LEU Chi-restraints excluded: chain C residue 760 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 480 ASN Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 760 PHE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 59 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082198 restraints weight = 63365.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.084340 restraints weight = 37218.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085730 restraints weight = 26902.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.086507 restraints weight = 22019.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087067 restraints weight = 19578.451| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 26368 Z= 0.272 Angle : 0.702 8.371 35964 Z= 0.363 Chirality : 0.042 0.195 4256 Planarity : 0.004 0.035 4416 Dihedral : 9.596 108.614 3924 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.98 % Allowed : 13.46 % Favored : 80.56 % 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: 0.44 (0.15), residues: 3160 helix: 1.16 (0.11), residues: 2284 sheet: 0.81 (0.44), residues: 140 loop : -2.61 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 884 TYR 0.021 0.002 TYR B 646 PHE 0.018 0.002 PHE D1012 TRP 0.021 0.002 TRP A 682 HIS 0.007 0.002 HIS D 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.27 (26364) covalent geometry : angle 0.70139 / 0.36 (35956) SS BOND : bond 0.00065 / 0.03 ( 4) SS BOND : angle 2.35639 / 1.17 ( 8) hydrogen bonds : bond 0.05807 / 4.03 ( 1708) hydrogen bonds : angle 4.37171 / 3.11 ( 5124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 298 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8395 (pp20) cc_final: 0.8109 (tm-30) REVERT: A 641 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8370 (mm-30) REVERT: A 667 GLN cc_start: 0.8626 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 701 PHE cc_start: 0.7451 (m-10) cc_final: 0.7037 (m-10) REVERT: A 782 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7834 (mm-30) REVERT: A 802 ASP cc_start: 0.8473 (t0) cc_final: 0.8266 (t0) REVERT: A 858 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8199 (ttp) REVERT: A 877 MET cc_start: 0.9376 (mmm) cc_final: 0.9073 (mmm) REVERT: B 133 MET cc_start: 0.8472 (mmm) cc_final: 0.8262 (mmm) REVERT: B 667 GLN cc_start: 0.8629 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 701 PHE cc_start: 0.7447 (m-10) cc_final: 0.6988 (m-10) REVERT: B 782 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 858 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8212 (ttp) REVERT: B 877 MET cc_start: 0.9377 (mmm) cc_final: 0.9073 (mmm) REVERT: B 969 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (mm) REVERT: C 667 GLN cc_start: 0.8624 (tm-30) cc_final: 0.7935 (tm-30) REVERT: C 701 PHE cc_start: 0.7465 (m-10) cc_final: 0.7033 (m-10) REVERT: C 782 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7849 (mm-30) REVERT: C 802 ASP cc_start: 0.8470 (t0) cc_final: 0.8259 (t0) REVERT: C 858 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8196 (ttp) REVERT: C 877 MET cc_start: 0.9391 (mmm) cc_final: 0.9064 (mmm) REVERT: D 641 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8363 (mm-30) REVERT: D 667 GLN cc_start: 0.8618 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 701 PHE cc_start: 0.7486 (m-10) cc_final: 0.7045 (m-10) REVERT: D 782 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8029 (mm-30) REVERT: D 802 ASP cc_start: 0.8463 (t0) cc_final: 0.8250 (t0) REVERT: D 858 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8202 (ttp) REVERT: D 877 MET cc_start: 0.9385 (mmm) cc_final: 0.9042 (mmm) outliers start: 140 outliers final: 92 residues processed: 407 average time/residue: 0.1408 time to fit residues: 98.9241 Evaluate side-chains 370 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 273 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 725 LEU Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 5 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 190 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 785 GLN A 844 HIS B 785 GLN B 844 HIS C 785 GLN C 844 HIS D 785 GLN D 844 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.086419 restraints weight = 62828.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086677 restraints weight = 39484.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086717 restraints weight = 32161.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086888 restraints weight = 29830.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087140 restraints weight = 27523.221| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26368 Z= 0.189 Angle : 0.603 7.830 35964 Z= 0.309 Chirality : 0.039 0.143 4256 Planarity : 0.003 0.033 4416 Dihedral : 8.915 101.677 3924 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.43 % Allowed : 15.26 % Favored : 79.32 % 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: 1.08 (0.15), residues: 3160 helix: 1.64 (0.11), residues: 2288 sheet: 0.80 (0.44), residues: 140 loop : -2.37 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1045 TYR 0.015 0.001 TYR C 646 PHE 0.015 0.001 PHE D1012 TRP 0.017 0.001 TRP B 682 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (26364) covalent geometry : angle 0.60265 / 0.31 (35956) SS BOND : bond 0.00036 / 0.02 ( 4) SS BOND : angle 1.79978 / 0.89 ( 8) hydrogen bonds : bond 0.04933 / 3.43 ( 1708) hydrogen bonds : angle 4.00106 / 2.85 ( 5124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 307 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: A 641 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8356 (mm-30) REVERT: A 667 GLN cc_start: 0.8600 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 782 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 877 MET cc_start: 0.9378 (mmm) cc_final: 0.9101 (mmm) REVERT: A 1058 MET cc_start: 0.9090 (mmm) cc_final: 0.8327 (mmt) REVERT: B 667 GLN cc_start: 0.8560 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 701 PHE cc_start: 0.7447 (m-10) cc_final: 0.7070 (m-10) REVERT: B 858 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8092 (ttt) REVERT: B 877 MET cc_start: 0.9396 (mmm) cc_final: 0.9125 (mmm) REVERT: B 1058 MET cc_start: 0.9111 (mmm) cc_final: 0.8370 (mmt) REVERT: C 207 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: C 667 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7813 (tm-30) REVERT: C 782 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8487 (mm-30) REVERT: C 858 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: C 877 MET cc_start: 0.9379 (mmm) cc_final: 0.9095 (mmm) REVERT: C 1058 MET cc_start: 0.9115 (mmm) cc_final: 0.8377 (mmt) REVERT: D 641 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8366 (mm-30) REVERT: D 667 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 701 PHE cc_start: 0.7448 (m-10) cc_final: 0.7073 (m-10) REVERT: D 782 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8519 (mm-30) REVERT: D 858 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8166 (ttt) REVERT: D 877 MET cc_start: 0.9372 (mmm) cc_final: 0.9087 (mmm) REVERT: D 1058 MET cc_start: 0.9110 (mmm) cc_final: 0.8374 (mmt) outliers start: 127 outliers final: 86 residues processed: 396 average time/residue: 0.1372 time to fit residues: 94.3503 Evaluate side-chains 378 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 287 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 147 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 324 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.112549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.080088 restraints weight = 63835.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.082268 restraints weight = 37939.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.083703 restraints weight = 27425.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084522 restraints weight = 22377.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085111 restraints weight = 19844.421| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 26368 Z= 0.209 Angle : 0.622 7.654 35964 Z= 0.317 Chirality : 0.040 0.143 4256 Planarity : 0.004 0.037 4416 Dihedral : 8.330 99.397 3924 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.03 % Allowed : 15.56 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.34 (0.15), residues: 3160 helix: 1.88 (0.11), residues: 2280 sheet: 0.22 (0.42), residues: 144 loop : -2.25 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1045 TYR 0.017 0.002 TYR A 646 PHE 0.026 0.002 PHE D 776 TRP 0.016 0.001 TRP B 682 HIS 0.005 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (26364) covalent geometry : angle 0.62153 / 0.32 (35956) SS BOND : bond 0.00065 / 0.03 ( 4) SS BOND : angle 1.80770 / 0.90 ( 8) hydrogen bonds : bond 0.05044 / 3.50 ( 1708) hydrogen bonds : angle 3.99083 / 2.84 ( 5124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 288 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8790 (tpp) cc_final: 0.8491 (ttm) REVERT: A 641 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8380 (mm-30) REVERT: A 667 GLN cc_start: 0.8785 (mm-40) cc_final: 0.7924 (tm-30) REVERT: A 877 MET cc_start: 0.9348 (mmm) cc_final: 0.8942 (mmm) REVERT: B 601 MET cc_start: 0.8787 (tpp) cc_final: 0.8486 (ttm) REVERT: B 667 GLN cc_start: 0.8783 (mm-40) cc_final: 0.7949 (tm-30) REVERT: B 697 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8844 (mp) REVERT: B 877 MET cc_start: 0.9345 (mmm) cc_final: 0.8935 (mmm) REVERT: C 207 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: C 601 MET cc_start: 0.8784 (tpp) cc_final: 0.8495 (ttm) REVERT: C 667 GLN cc_start: 0.8781 (mm-40) cc_final: 0.7955 (tm-30) REVERT: C 858 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8048 (ttt) REVERT: C 877 MET cc_start: 0.9329 (mmm) cc_final: 0.8940 (mmm) REVERT: D 601 MET cc_start: 0.8795 (tpp) cc_final: 0.8492 (ttm) REVERT: D 641 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8374 (mm-30) REVERT: D 667 GLN cc_start: 0.8780 (mm-40) cc_final: 0.7930 (tm-30) REVERT: D 697 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8855 (mp) REVERT: D 858 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8049 (ttt) REVERT: D 877 MET cc_start: 0.9328 (mmm) cc_final: 0.8929 (mmm) REVERT: D 1003 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8484 (tm-30) outliers start: 141 outliers final: 106 residues processed: 390 average time/residue: 0.1288 time to fit residues: 87.3425 Evaluate side-chains 382 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 271 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 188 optimal weight: 9.9990 chunk 334 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 168 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080738 restraints weight = 63816.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.081932 restraints weight = 41987.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.081813 restraints weight = 30177.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082144 restraints weight = 31854.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082219 restraints weight = 27312.656| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 26368 Z= 0.252 Angle : 0.668 7.820 35964 Z= 0.341 Chirality : 0.041 0.147 4256 Planarity : 0.004 0.036 4416 Dihedral : 7.982 100.045 3924 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 6.20 % Allowed : 16.79 % Favored : 77.01 % 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: 1.34 (0.15), residues: 3160 helix: 1.89 (0.11), residues: 2268 sheet: -0.13 (0.41), residues: 144 loop : -2.11 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 884 TYR 0.020 0.002 TYR D 646 PHE 0.014 0.002 PHE C1012 TRP 0.017 0.002 TRP D 682 HIS 0.005 0.002 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (26364) covalent geometry : angle 0.66700 / 0.34 (35956) SS BOND : bond 0.00076 / 0.04 ( 4) SS BOND : angle 1.85807 / 0.93 ( 8) hydrogen bonds : bond 0.05343 / 3.71 ( 1708) hydrogen bonds : angle 4.16308 / 2.96 ( 5124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 263 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8782 (tpp) cc_final: 0.8489 (ttm) REVERT: A 641 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 667 GLN cc_start: 0.8767 (mm-40) cc_final: 0.7991 (tm-30) REVERT: A 807 PHE cc_start: 0.8782 (m-80) cc_final: 0.8557 (m-10) REVERT: A 858 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8320 (ttt) REVERT: A 862 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: A 877 MET cc_start: 0.9372 (mmm) cc_final: 0.8923 (mmm) REVERT: A 1058 MET cc_start: 0.9259 (mmp) cc_final: 0.8995 (mmp) REVERT: B 601 MET cc_start: 0.8792 (tpp) cc_final: 0.8497 (ttm) REVERT: B 697 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8644 (mp) REVERT: B 807 PHE cc_start: 0.8809 (m-80) cc_final: 0.8575 (m-10) REVERT: B 858 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8336 (ttt) REVERT: B 862 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: B 877 MET cc_start: 0.9374 (mmm) cc_final: 0.9011 (mmm) REVERT: B 1058 MET cc_start: 0.9139 (mmm) cc_final: 0.8442 (mmt) REVERT: C 601 MET cc_start: 0.8785 (tpp) cc_final: 0.8502 (ttm) REVERT: C 807 PHE cc_start: 0.8787 (m-80) cc_final: 0.8557 (m-10) REVERT: C 858 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8293 (ttt) REVERT: C 862 MET cc_start: 0.8868 (mtm) cc_final: 0.8651 (mtt) REVERT: C 877 MET cc_start: 0.9368 (mmm) cc_final: 0.8928 (mmm) REVERT: C 1058 MET cc_start: 0.9142 (mmm) cc_final: 0.8435 (mmt) REVERT: D 601 MET cc_start: 0.8773 (tpp) cc_final: 0.8491 (ttm) REVERT: D 641 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8375 (mm-30) REVERT: D 667 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8033 (tm-30) REVERT: D 697 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8648 (mp) REVERT: D 807 PHE cc_start: 0.8804 (m-80) cc_final: 0.8582 (m-10) REVERT: D 858 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8318 (ttp) REVERT: D 862 MET cc_start: 0.8877 (mtm) cc_final: 0.8654 (mtt) REVERT: D 877 MET cc_start: 0.9364 (mmm) cc_final: 0.8982 (mmm) REVERT: D 1058 MET cc_start: 0.9147 (mmm) cc_final: 0.8434 (mmt) outliers start: 145 outliers final: 112 residues processed: 365 average time/residue: 0.1376 time to fit residues: 87.7728 Evaluate side-chains 378 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 258 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 637 GLU Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 707 CYS Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 902 VAL Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 975 VAL Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 152 optimal weight: 0.7980 chunk 276 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 123 optimal weight: 0.0060 chunk 251 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 HIS ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 HIS ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 HIS ** D 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.082850 restraints weight = 63067.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085142 restraints weight = 36872.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086654 restraints weight = 26343.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087619 restraints weight = 21311.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088177 restraints weight = 18674.603| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26368 Z= 0.126 Angle : 0.552 9.182 35964 Z= 0.279 Chirality : 0.037 0.146 4256 Planarity : 0.003 0.036 4416 Dihedral : 7.332 93.370 3924 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.70 % Allowed : 20.09 % Favored : 75.21 % 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: 1.76 (0.15), residues: 3160 helix: 2.22 (0.11), residues: 2272 sheet: 0.11 (0.43), residues: 144 loop : -2.12 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1045 TYR 0.012 0.001 TYR B 835 PHE 0.027 0.001 PHE A 776 TRP 0.018 0.001 TRP C 740 HIS 0.003 0.001 HIS D 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (26364) covalent geometry : angle 0.55191 / 0.28 (35956) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 1.15162 / 0.58 ( 8) hydrogen bonds : bond 0.04058 / 2.82 ( 1708) hydrogen bonds : angle 3.67433 / 2.62 ( 5124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 329 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8353 (mm-30) REVERT: A 662 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 667 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 707 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7439 (m) REVERT: A 858 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8023 (ttt) REVERT: A 862 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: A 877 MET cc_start: 0.9256 (mmm) cc_final: 0.8677 (tpp) REVERT: B 667 GLN cc_start: 0.8793 (mm-40) cc_final: 0.7895 (tm-30) REVERT: B 782 GLU cc_start: 0.8864 (tp30) cc_final: 0.8415 (tp30) REVERT: B 858 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8048 (ttt) REVERT: B 862 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8249 (mtt) REVERT: B 877 MET cc_start: 0.9263 (mmm) cc_final: 0.8684 (tpp) REVERT: B 1058 MET cc_start: 0.9200 (mmm) cc_final: 0.8579 (mmt) REVERT: C 667 GLN cc_start: 0.8790 (mm-40) cc_final: 0.7899 (tm-30) REVERT: C 782 GLU cc_start: 0.8871 (tp30) cc_final: 0.8301 (mm-30) REVERT: C 858 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7985 (ttt) REVERT: C 877 MET cc_start: 0.9262 (mmm) cc_final: 0.8663 (tpp) REVERT: C 1058 MET cc_start: 0.9196 (mmm) cc_final: 0.8571 (mmt) REVERT: D 641 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8371 (mm-30) REVERT: D 667 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: D 782 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8234 (mm-30) REVERT: D 802 ASP cc_start: 0.8260 (t0) cc_final: 0.7886 (t0) REVERT: D 858 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7980 (ttt) REVERT: D 877 MET cc_start: 0.9262 (mmm) cc_final: 0.8664 (tpt) REVERT: D 1058 MET cc_start: 0.9158 (mmm) cc_final: 0.8514 (mmt) outliers start: 110 outliers final: 65 residues processed: 415 average time/residue: 0.1331 time to fit residues: 95.0056 Evaluate side-chains 346 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 272 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 271 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 250 optimal weight: 0.4980 chunk 194 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 24 optimal weight: 0.0770 chunk 101 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 ASN ** 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 = 0.3585 r_free = 0.3585 target = 0.114874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.082267 restraints weight = 63095.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.084500 restraints weight = 37263.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085964 restraints weight = 26893.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086800 restraints weight = 21915.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087487 restraints weight = 19353.914| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 26368 Z= 0.132 Angle : 0.569 8.627 35964 Z= 0.286 Chirality : 0.038 0.175 4256 Planarity : 0.003 0.037 4416 Dihedral : 7.032 83.894 3924 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.59 % Allowed : 21.88 % Favored : 74.53 % 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: 1.84 (0.15), residues: 3160 helix: 2.28 (0.11), residues: 2276 sheet: 0.17 (0.43), residues: 144 loop : -2.12 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1045 TYR 0.016 0.001 TYR D 646 PHE 0.012 0.001 PHE B1012 TRP 0.018 0.001 TRP C 740 HIS 0.003 0.001 HIS B 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (26364) covalent geometry : angle 0.56909 / 0.29 (35956) SS BOND : bond 0.00029 / 0.01 ( 4) SS BOND : angle 1.09114 / 0.55 ( 8) hydrogen bonds : bond 0.04026 / 2.80 ( 1708) hydrogen bonds : angle 3.63784 / 2.59 ( 5124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 313 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8735 (tpp) cc_final: 0.8520 (ttm) REVERT: A 641 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8426 (mm-30) REVERT: A 667 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: A 707 CYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7535 (m) REVERT: A 858 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7997 (ttt) REVERT: A 862 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: A 877 MET cc_start: 0.9225 (mmm) cc_final: 0.8653 (tpp) REVERT: B 601 MET cc_start: 0.8742 (tpp) cc_final: 0.8517 (ttm) REVERT: B 662 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 667 GLN cc_start: 0.8767 (mm-40) cc_final: 0.7820 (tm-30) REVERT: B 858 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8023 (ttt) REVERT: B 862 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8328 (mtt) REVERT: B 877 MET cc_start: 0.9229 (mmm) cc_final: 0.8651 (tpp) REVERT: B 1058 MET cc_start: 0.9131 (mmm) cc_final: 0.8545 (mmt) REVERT: C 601 MET cc_start: 0.8727 (tpp) cc_final: 0.8508 (ttm) REVERT: C 662 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 667 GLN cc_start: 0.8774 (mm-40) cc_final: 0.7843 (tm-30) REVERT: C 858 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8053 (ttt) REVERT: C 877 MET cc_start: 0.9229 (mmm) cc_final: 0.8722 (tpp) REVERT: C 1003 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 1058 MET cc_start: 0.9130 (mmm) cc_final: 0.8474 (mmt) REVERT: D 601 MET cc_start: 0.8736 (tpp) cc_final: 0.8525 (ttm) REVERT: D 641 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8415 (mm-30) REVERT: D 662 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8075 (mm-30) REVERT: D 667 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: D 782 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8234 (mm-30) REVERT: D 802 ASP cc_start: 0.8299 (t0) cc_final: 0.7932 (t0) REVERT: D 858 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8068 (ttp) REVERT: D 877 MET cc_start: 0.9228 (mmm) cc_final: 0.8642 (tpp) REVERT: D 1003 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 1058 MET cc_start: 0.9136 (mmm) cc_final: 0.8546 (mmt) outliers start: 84 outliers final: 70 residues processed: 373 average time/residue: 0.1347 time to fit residues: 87.9167 Evaluate side-chains 374 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 295 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 858 MET Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 858 MET Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 5 optimal weight: 0.2980 chunk 317 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 274 optimal weight: 6.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 GLN ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 ASN ** 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 = 0.3526 r_free = 0.3526 target = 0.110800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078946 restraints weight = 64058.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.081718 restraints weight = 39163.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.082129 restraints weight = 24609.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.082667 restraints weight = 23175.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.082545 restraints weight = 20416.640| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 26368 Z= 0.267 Angle : 0.698 8.127 35964 Z= 0.355 Chirality : 0.042 0.207 4256 Planarity : 0.004 0.035 4416 Dihedral : 7.271 76.850 3924 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.53 % Allowed : 21.50 % Favored : 73.97 % 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: 1.51 (0.15), residues: 3160 helix: 2.03 (0.11), residues: 2288 sheet: -0.03 (0.43), residues: 144 loop : -2.26 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 884 TYR 0.019 0.002 TYR C 646 PHE 0.018 0.002 PHE A 776 TRP 0.030 0.002 TRP A 740 HIS 0.005 0.002 HIS D 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (26364) covalent geometry : angle 0.69737 / 0.36 (35956) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 1.79627 / 0.91 ( 8) hydrogen bonds : bond 0.05262 / 3.65 ( 1708) hydrogen bonds : angle 4.15407 / 2.96 ( 5124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 260 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8795 (tpp) cc_final: 0.8583 (ttm) REVERT: A 641 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 662 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8124 (mm-30) REVERT: A 667 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: A 858 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8356 (ttt) REVERT: A 862 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: A 877 MET cc_start: 0.9364 (mmm) cc_final: 0.8953 (mmm) REVERT: B 601 MET cc_start: 0.8803 (tpp) cc_final: 0.8582 (ttm) REVERT: B 667 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8085 (tm-30) REVERT: B 782 GLU cc_start: 0.8921 (tp30) cc_final: 0.8366 (mm-30) REVERT: B 858 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8358 (ttt) REVERT: B 862 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: B 877 MET cc_start: 0.9358 (mmm) cc_final: 0.8956 (mmm) REVERT: C 601 MET cc_start: 0.8807 (tpp) cc_final: 0.8593 (ttm) REVERT: C 667 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8098 (tm-30) REVERT: C 782 GLU cc_start: 0.8921 (tp30) cc_final: 0.8371 (mm-30) REVERT: C 877 MET cc_start: 0.9192 (mmm) cc_final: 0.8818 (tpp) REVERT: D 601 MET cc_start: 0.8795 (tpp) cc_final: 0.8588 (ttm) REVERT: D 641 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8421 (mm-30) REVERT: D 667 GLN cc_start: 0.8803 (mm-40) cc_final: 0.7912 (tm-30) REVERT: D 877 MET cc_start: 0.9346 (mmm) cc_final: 0.8927 (mmm) REVERT: D 1048 ASP cc_start: 0.8589 (m-30) cc_final: 0.8364 (m-30) outliers start: 106 outliers final: 82 residues processed: 336 average time/residue: 0.1451 time to fit residues: 84.8016 Evaluate side-chains 347 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 260 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 453 TRP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 453 TRP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 689 ASP Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 847 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 453 TRP Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 689 ASP Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 127 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 209 optimal weight: 0.2980 chunk 275 optimal weight: 40.0000 chunk 146 optimal weight: 3.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 GLN ** D 851 ASN ** 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 = 0.3571 r_free = 0.3571 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081152 restraints weight = 63319.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.083360 restraints weight = 37528.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.084786 restraints weight = 27202.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085726 restraints weight = 22220.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086249 restraints weight = 19561.901| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26368 Z= 0.152 Angle : 0.605 9.602 35964 Z= 0.305 Chirality : 0.039 0.239 4256 Planarity : 0.003 0.037 4416 Dihedral : 7.015 75.769 3924 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.46 % Allowed : 22.86 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.15), residues: 3160 helix: 2.16 (0.11), residues: 2292 sheet: 0.10 (0.43), residues: 144 loop : -2.18 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1045 TYR 0.017 0.001 TYR C 646 PHE 0.013 0.001 PHE D1012 TRP 0.030 0.001 TRP A 740 HIS 0.003 0.001 HIS A 844 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (26364) covalent geometry : angle 0.60452 / 0.31 (35956) SS BOND : bond 0.00015 / 0.01 ( 4) SS BOND : angle 1.17863 / 0.59 ( 8) hydrogen bonds : bond 0.04378 / 3.04 ( 1708) hydrogen bonds : angle 3.80135 / 2.71 ( 5124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 286 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 662 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 667 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: A 858 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8183 (ttt) REVERT: A 862 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: A 877 MET cc_start: 0.9292 (mmm) cc_final: 0.8754 (tpp) REVERT: B 667 GLN cc_start: 0.8779 (mm-40) cc_final: 0.7865 (tm-30) REVERT: B 782 GLU cc_start: 0.8826 (tp30) cc_final: 0.8285 (mm-30) REVERT: B 858 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8212 (ttt) REVERT: B 862 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8311 (mtt) REVERT: B 877 MET cc_start: 0.9292 (mmm) cc_final: 0.8756 (tpp) REVERT: B 1058 MET cc_start: 0.9135 (mmm) cc_final: 0.8782 (mmt) REVERT: C 667 GLN cc_start: 0.8779 (mm-40) cc_final: 0.7864 (tm-30) REVERT: C 782 GLU cc_start: 0.8816 (tp30) cc_final: 0.8325 (mm-30) REVERT: C 858 MET cc_start: 0.8764 (ttm) cc_final: 0.8271 (ttt) REVERT: C 877 MET cc_start: 0.9113 (mmm) cc_final: 0.8762 (tpp) REVERT: C 1058 MET cc_start: 0.9106 (mmm) cc_final: 0.8755 (mmt) REVERT: D 641 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8415 (mm-30) REVERT: D 667 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: D 858 MET cc_start: 0.8759 (ttm) cc_final: 0.8260 (ttt) REVERT: D 877 MET cc_start: 0.9317 (mmm) cc_final: 0.8704 (tpt) REVERT: D 969 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8492 (mm) REVERT: D 1058 MET cc_start: 0.9122 (mmm) cc_final: 0.8739 (mmt) outliers start: 81 outliers final: 63 residues processed: 348 average time/residue: 0.1413 time to fit residues: 85.6144 Evaluate side-chains 351 residues out of total 2956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 281 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 667 GLN Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 707 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 858 MET Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 895 TRP Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 993 TRP Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 637 GLU Chi-restraints excluded: chain B residue 683 TYR Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 847 THR Chi-restraints excluded: chain B residue 858 MET Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 TRP Chi-restraints excluded: chain B residue 968 ILE Chi-restraints excluded: chain B residue 993 TRP Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 683 TYR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 895 TRP Chi-restraints excluded: chain C residue 968 ILE Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 993 TRP Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 667 GLN Chi-restraints excluded: chain D residue 683 TYR Chi-restraints excluded: chain D residue 749 LEU Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 847 THR Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 895 TRP Chi-restraints excluded: chain D residue 968 ILE Chi-restraints excluded: chain D residue 969 LEU Chi-restraints excluded: chain D residue 993 TRP Chi-restraints excluded: chain D residue 1000 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 37 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 137 optimal weight: 0.3980 chunk 268 optimal weight: 0.0770 chunk 306 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.085202 restraints weight = 62687.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.087563 restraints weight = 36545.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089118 restraints weight = 26131.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090021 restraints weight = 21208.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090739 restraints weight = 18649.915| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26368 Z= 0.107 Angle : 0.576 9.313 35964 Z= 0.286 Chirality : 0.037 0.206 4256 Planarity : 0.003 0.038 4416 Dihedral : 6.184 73.090 3916 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.56 % Allowed : 24.02 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.96 (0.15), residues: 3160 helix: 2.38 (0.11), residues: 2272 sheet: 0.44 (0.44), residues: 144 loop : -2.13 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1045 TYR 0.018 0.001 TYR C 646 PHE 0.019 0.001 PHE D 776 TRP 0.018 0.002 TRP C 740 HIS 0.001 0.001 HIS C 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (26364) covalent geometry : angle 0.57620 / 0.29 (35956) SS BOND : bond 0.00044 / 0.02 ( 4) SS BOND : angle 0.67378 / 0.34 ( 8) hydrogen bonds : bond 0.03435 / 2.39 ( 1708) hydrogen bonds : angle 3.50787 / 2.50 ( 5124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4178.47 seconds wall clock time: 72 minutes 52.31 seconds (4372.31 seconds total)