Starting phenix.real_space_refine on Thu Mar 5 14:58:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nr4_0489/03_2026/6nr4_0489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nr4_0489/03_2026/6nr4_0489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nr4_0489/03_2026/6nr4_0489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nr4_0489/03_2026/6nr4_0489_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nr4_0489/03_2026/6nr4_0489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nr4_0489/03_2026/6nr4_0489.map" } resolution = 4.3 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= 0.008 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: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 15272 2.51 5 N 3872 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23264 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 5696 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 18, 'TRANS': 761} Chain breaks: 20 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 964 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'UNK:plan-1': 21, 'TYR:plan': 7, 'ARG:plan': 16, 'ASP:plan': 20, 'GLU:plan': 26, 'GLN:plan1': 5, 'HIS:plan': 5, 'ASN:plan1': 8, 'PHE:plan': 11, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 467 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 Restraints were copied for chains: B, C, D Time building chain proxies: 5.47, per 1000 atoms: 0.24 Number of scatterers: 23264 At special positions: 0 Unit cell: (150.12, 150.12, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4008 8.00 N 3872 7.00 C 15272 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: 1.75 Conformation dependent library (CDL) restraints added in 888.9 milliseconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6232 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 8 sheets defined 80.0% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.003A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.829A pdb=" N GLU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.767A pdb=" N ASN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 378 through 387 removed outlier: 4.308A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.016A pdb=" N GLN A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 431 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 454 through 468 removed outlier: 3.803A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 removed outlier: 3.664A pdb=" N VAL A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.875A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.763A pdb=" N ASN A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.625A pdb=" N ALA A 563 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.805A pdb=" N SER A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 3.871A 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 Processing helix chain 'A' and resid 607 through 636 removed outlier: 3.731A pdb=" N ALA A 611 " --> pdb=" O ASP A 607 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 636 " --> pdb=" O CYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 removed outlier: 3.538A pdb=" N ALA A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 4.332A pdb=" N PHE A 668 " --> pdb=" O ASP A 665 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 669 " --> pdb=" O GLN A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 671 through 683 removed outlier: 3.762A pdb=" N GLN A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.967A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.676A pdb=" N GLY A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 732 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 790 removed outlier: 3.827A pdb=" N ILE A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET A 788 " --> pdb=" O ARG A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 removed outlier: 3.600A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 817 " --> pdb=" O ILE A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 851 Processing helix chain 'A' and resid 854 through 888 removed outlier: 4.621A pdb=" N ILE A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 910 removed outlier: 4.125A pdb=" N SER A 901 " --> pdb=" O TRP A 897 " (cutoff:3.500A) Proline residue: A 906 - end of helix Processing helix chain 'A' and resid 954 through 978 removed outlier: 3.524A pdb=" N ASN A 972 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 3.881A pdb=" N PHE A 995 " --> pdb=" O GLN A 991 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 996 " --> pdb=" O VAL A 992 " (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 1022 removed outlier: 3.688A pdb=" N ALA A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1068 removed outlier: 3.724A pdb=" N LYS A1065 " --> pdb=" O ASN A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1100 removed outlier: 3.630A pdb=" N UNK A1100 " --> pdb=" O UNK A1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 203 removed outlier: 4.002A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.829A pdb=" N GLU B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.767A pdb=" N ASN B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.309A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 425 through 436 removed outlier: 4.017A pdb=" N GLN B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 431 " --> pdb=" O ASN B 427 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 454 through 468 removed outlier: 3.803A pdb=" N LEU B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.664A pdb=" N VAL B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.875A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.763A pdb=" N ASN B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.624A pdb=" N ALA B 563 " --> pdb=" O HIS B 559 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.805A pdb=" N SER B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 3.870A 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 Processing helix chain 'B' and resid 607 through 636 removed outlier: 3.731A pdb=" N ALA B 611 " --> pdb=" O ASP B 607 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 613 " --> pdb=" O ASN B 609 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP B 636 " --> pdb=" O CYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.539A pdb=" N ALA B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 664 Processing helix chain 'B' and resid 665 through 669 removed outlier: 4.332A pdb=" N PHE B 668 " --> pdb=" O ASP B 665 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 669 " --> pdb=" O GLN B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 671 through 683 removed outlier: 3.762A pdb=" N GLN B 675 " --> pdb=" O GLN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.967A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.676A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 732 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 790 removed outlier: 3.827A pdb=" N ILE B 769 " --> pdb=" O THR B 765 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 788 " --> pdb=" O ARG B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 817 removed outlier: 3.601A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 817 " --> pdb=" O ILE B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 851 Processing helix chain 'B' and resid 854 through 888 removed outlier: 4.621A pdb=" N ILE B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 865 " --> pdb=" O ARG B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 910 removed outlier: 4.125A pdb=" N SER B 901 " --> pdb=" O TRP B 897 " (cutoff:3.500A) Proline residue: B 906 - end of helix Processing helix chain 'B' and resid 954 through 978 removed outlier: 3.524A pdb=" N ASN B 972 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1008 removed outlier: 3.882A pdb=" N PHE B 995 " --> pdb=" O GLN B 991 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 996 " --> pdb=" O VAL B 992 " (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 1022 removed outlier: 3.689A pdb=" N ALA B1018 " --> pdb=" O PHE B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1067 removed outlier: 3.724A pdb=" N LYS B1065 " --> pdb=" O ASN B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1078 through 1100 removed outlier: 3.630A pdb=" N UNK B1100 " --> pdb=" O UNK B1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 203 removed outlier: 4.002A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.829A pdb=" N GLU C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.767A pdb=" N ASN C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 378 through 387 removed outlier: 4.309A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 425 through 436 removed outlier: 4.017A pdb=" N GLN C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 431 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 454 through 468 removed outlier: 3.802A pdb=" N LEU C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 removed outlier: 3.664A pdb=" N VAL C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 500 removed outlier: 3.875A pdb=" N ASN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.763A pdb=" N ASN C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.624A pdb=" N ALA C 563 " --> pdb=" O HIS C 559 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 571 " --> pdb=" O TRP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 581 removed outlier: 3.805A pdb=" N SER C 577 " --> pdb=" O LYS C 573 " (cutoff:3.500A) removed outlier: 3.870A 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 Processing helix chain 'C' and resid 607 through 636 removed outlier: 3.731A pdb=" N ALA C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 613 " --> pdb=" O ASN C 609 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP C 636 " --> pdb=" O CYS C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 645 removed outlier: 3.539A pdb=" N ALA C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'C' and resid 665 through 669 removed outlier: 4.332A pdb=" N PHE C 668 " --> pdb=" O ASP C 665 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 669 " --> pdb=" O GLN C 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 669' Processing helix chain 'C' and resid 671 through 683 removed outlier: 3.762A pdb=" N GLN C 675 " --> pdb=" O GLN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.967A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 708 removed outlier: 3.676A pdb=" N GLY C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 732 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 790 removed outlier: 3.827A pdb=" N ILE C 769 " --> pdb=" O THR C 765 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET C 788 " --> pdb=" O ARG C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 817 removed outlier: 3.601A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU C 817 " --> pdb=" O ILE C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 851 Processing helix chain 'C' and resid 854 through 888 removed outlier: 4.621A pdb=" N ILE C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP C 865 " --> pdb=" O ARG C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 910 removed outlier: 4.124A pdb=" N SER C 901 " --> pdb=" O TRP C 897 " (cutoff:3.500A) Proline residue: C 906 - end of helix Processing helix chain 'C' and resid 954 through 978 removed outlier: 3.524A pdb=" N ASN C 972 " --> pdb=" O ILE C 968 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1008 removed outlier: 3.881A pdb=" N PHE C 995 " --> pdb=" O GLN C 991 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 996 " --> pdb=" O VAL C 992 " (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 1022 removed outlier: 3.689A pdb=" N ALA C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1068 removed outlier: 3.724A pdb=" N LYS C1065 " --> pdb=" O ASN C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1078 through 1100 removed outlier: 3.630A pdb=" N UNK C1100 " --> pdb=" O UNK C1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 203 removed outlier: 4.002A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.829A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.767A pdb=" N ASN D 317 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 352 through 361 Processing helix chain 'D' and resid 378 through 387 removed outlier: 4.309A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 420 Processing helix chain 'D' and resid 425 through 436 removed outlier: 4.017A pdb=" N GLN D 429 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 431 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 454 through 468 removed outlier: 3.803A pdb=" N LEU D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS D 468 " --> pdb=" O THR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 removed outlier: 3.664A pdb=" N VAL D 474 " --> pdb=" O ARG D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.876A pdb=" N ASN D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 516 removed outlier: 3.763A pdb=" N ASN D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.624A pdb=" N ALA D 563 " --> pdb=" O HIS D 559 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 571 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.805A pdb=" N SER D 577 " --> pdb=" O LYS D 573 " (cutoff:3.500A) removed outlier: 3.870A 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 Processing helix chain 'D' and resid 607 through 636 removed outlier: 3.731A pdb=" N ALA D 611 " --> pdb=" O ASP D 607 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 613 " --> pdb=" O ASN D 609 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG D 624 " --> pdb=" O GLU D 620 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 removed outlier: 3.539A pdb=" N ALA D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 664 Processing helix chain 'D' and resid 665 through 669 removed outlier: 4.332A pdb=" N PHE D 668 " --> pdb=" O ASP D 665 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 669 " --> pdb=" O GLN D 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 665 through 669' Processing helix chain 'D' and resid 671 through 683 removed outlier: 3.762A pdb=" N GLN D 675 " --> pdb=" O GLN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.967A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 708 removed outlier: 3.676A pdb=" N GLY D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 790 removed outlier: 3.827A pdb=" N ILE D 769 " --> pdb=" O THR D 765 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET D 788 " --> pdb=" O ARG D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 817 removed outlier: 3.601A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU D 817 " --> pdb=" O ILE D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 851 Processing helix chain 'D' and resid 854 through 888 removed outlier: 4.621A pdb=" N ILE D 864 " --> pdb=" O GLN D 860 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP D 865 " --> pdb=" O ARG D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 910 removed outlier: 4.125A pdb=" N SER D 901 " --> pdb=" O TRP D 897 " (cutoff:3.500A) Proline residue: D 906 - end of helix Processing helix chain 'D' and resid 954 through 978 removed outlier: 3.524A pdb=" N ASN D 972 " --> pdb=" O ILE D 968 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 978 " --> pdb=" O LEU D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1008 removed outlier: 3.881A pdb=" N PHE D 995 " --> pdb=" O GLN D 991 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D 996 " --> pdb=" O VAL D 992 " (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 1022 removed outlier: 3.689A pdb=" N ALA D1018 " --> pdb=" O PHE D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1067 removed outlier: 3.724A pdb=" N LYS D1065 " --> pdb=" O ASN D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1100 removed outlier: 3.630A pdb=" N UNK D1100 " --> pdb=" O UNK D1096 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.847A pdb=" N UNK A 108 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A 117 " --> pdb=" O LEU A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 5.759A pdb=" N ILE A 179 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 145 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL A 329 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA A 305 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.847A pdb=" N UNK B 108 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 117 " --> pdb=" O LEU B 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210 removed outlier: 5.759A pdb=" N ILE B 179 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 145 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL B 329 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA B 305 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.847A pdb=" N UNK C 108 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 117 " --> pdb=" O LEU C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210 removed outlier: 5.759A pdb=" N ILE C 179 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL C 145 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL C 329 " --> pdb=" O CYS C 303 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA C 305 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.847A pdb=" N UNK D 108 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR D 117 " --> pdb=" O LEU D 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210 removed outlier: 5.760A pdb=" N ILE D 179 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL D 145 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N CYS D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL D 329 " --> pdb=" O CYS D 303 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) 1602 hydrogen bonds defined for protein. 4806 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: 4.18 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7236 1.34 - 1.46: 5680 1.46 - 1.58: 10636 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 23720 Sorted by residual: bond pdb=" C GLU A 905 " pdb=" N PRO A 906 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.38e-02 5.25e+03 7.06e+00 bond pdb=" C GLU C 905 " pdb=" N PRO C 906 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.38e-02 5.25e+03 7.06e+00 bond pdb=" C GLU D 905 " pdb=" N PRO D 906 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.38e-02 5.25e+03 7.02e+00 bond pdb=" C GLU B 905 " pdb=" N PRO B 906 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.38e-02 5.25e+03 7.02e+00 bond pdb=" C LYS A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.23e-02 6.61e+03 3.22e+00 ... (remaining 23715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 31148 2.12 - 4.25: 1067 4.25 - 6.37: 125 6.37 - 8.49: 32 8.49 - 10.61: 12 Bond angle restraints: 32384 Sorted by residual: angle pdb=" N MET A 977 " pdb=" CA MET A 977 " pdb=" C MET A 977 " ideal model delta sigma weight residual 111.14 116.72 -5.58 1.08e+00 8.57e-01 2.67e+01 angle pdb=" N MET B 977 " pdb=" CA MET B 977 " pdb=" C MET B 977 " ideal model delta sigma weight residual 111.14 116.72 -5.58 1.08e+00 8.57e-01 2.67e+01 angle pdb=" N MET C 977 " pdb=" CA MET C 977 " pdb=" C MET C 977 " ideal model delta sigma weight residual 111.14 116.72 -5.58 1.08e+00 8.57e-01 2.67e+01 angle pdb=" N MET D 977 " pdb=" CA MET D 977 " pdb=" C MET D 977 " ideal model delta sigma weight residual 111.14 116.71 -5.57 1.08e+00 8.57e-01 2.66e+01 angle pdb=" N PHE A 668 " pdb=" CA PHE A 668 " pdb=" C PHE A 668 " ideal model delta sigma weight residual 113.88 107.92 5.96 1.23e+00 6.61e-01 2.35e+01 ... (remaining 32379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 12820 14.37 - 28.74: 692 28.74 - 43.10: 168 43.10 - 57.47: 20 57.47 - 71.84: 4 Dihedral angle restraints: 13704 sinusoidal: 4244 harmonic: 9460 Sorted by residual: dihedral pdb=" CA HIS B 136 " pdb=" C HIS B 136 " pdb=" N TRP B 137 " pdb=" CA TRP B 137 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA HIS D 136 " pdb=" C HIS D 136 " pdb=" N TRP D 137 " pdb=" CA TRP D 137 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA HIS A 136 " pdb=" C HIS A 136 " pdb=" N TRP A 137 " pdb=" CA TRP A 137 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 13701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3570 0.079 - 0.158: 355 0.158 - 0.237: 23 0.237 - 0.315: 0 0.315 - 0.394: 4 Chirality restraints: 3952 Sorted by residual: chirality pdb=" CB ILE A 146 " pdb=" CA ILE A 146 " pdb=" CG1 ILE A 146 " pdb=" CG2 ILE A 146 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CB ILE D 146 " pdb=" CA ILE D 146 " pdb=" CG1 ILE D 146 " pdb=" CG2 ILE D 146 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB ILE C 146 " pdb=" CA ILE C 146 " pdb=" CG1 ILE C 146 " pdb=" CG2 ILE C 146 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3949 not shown) Planarity restraints: 3988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 993 " 0.007 2.00e-02 2.50e+03 1.52e-02 5.79e+00 pdb=" CG TRP D 993 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP D 993 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 993 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 993 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP D 993 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 993 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 993 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 993 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 993 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 993 " -0.007 2.00e-02 2.50e+03 1.52e-02 5.79e+00 pdb=" CG TRP B 993 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 993 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 993 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 993 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP B 993 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 993 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 993 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 993 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 993 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 993 " -0.007 2.00e-02 2.50e+03 1.52e-02 5.78e+00 pdb=" CG TRP C 993 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 993 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 993 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 993 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP C 993 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 993 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 993 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 993 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 993 " -0.003 2.00e-02 2.50e+03 ... (remaining 3985 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7507 2.84 - 3.35: 21986 3.35 - 3.87: 35969 3.87 - 4.38: 37386 4.38 - 4.90: 63835 Nonbonded interactions: 166683 Sorted by model distance: nonbonded pdb=" O LEU A 592 " pdb=" OG SER A 595 " model vdw 2.319 3.040 nonbonded pdb=" O LEU D 592 " pdb=" OG SER D 595 " model vdw 2.319 3.040 nonbonded pdb=" O LEU B 592 " pdb=" OG SER B 595 " model vdw 2.319 3.040 nonbonded pdb=" O LEU C 592 " pdb=" OG SER C 595 " model vdw 2.319 3.040 nonbonded pdb=" OG SER C 409 " pdb=" NE2 GLN C 438 " model vdw 2.362 3.120 ... (remaining 166678 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: 0.06 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.006 0.052 23724 Z= 0.275 Angle : 0.935 10.614 32392 Z= 0.533 Chirality : 0.050 0.394 3952 Planarity : 0.006 0.052 3988 Dihedral : 9.964 71.838 7460 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.39 % Allowed : 5.12 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.12), residues: 2884 helix: -1.75 (0.09), residues: 2140 sheet: -0.71 (0.48), residues: 108 loop : -3.13 (0.19), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 664 TYR 0.019 0.002 TYR D1004 PHE 0.030 0.003 PHE A 477 TRP 0.035 0.003 TRP B 137 HIS 0.007 0.002 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00590 (23720) covalent geometry : angle 0.93390 (32384) SS BOND : bond 0.00031 ( 4) SS BOND : angle 3.00380 ( 8) hydrogen bonds : bond 0.14169 ( 1602) hydrogen bonds : angle 5.72028 ( 4806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 745 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7136 (mmm) cc_final: 0.6845 (mtt) REVERT: A 404 VAL cc_start: 0.8666 (t) cc_final: 0.8240 (t) REVERT: A 515 SER cc_start: 0.9358 (p) cc_final: 0.8741 (t) REVERT: A 598 LEU cc_start: 0.9186 (mt) cc_final: 0.8960 (mt) REVERT: A 605 LYS cc_start: 0.8740 (mttt) cc_final: 0.8258 (mttm) REVERT: A 666 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7400 (mm110) REVERT: A 693 TRP cc_start: 0.7942 (p-90) cc_final: 0.7294 (p-90) REVERT: A 757 LEU cc_start: 0.8075 (mt) cc_final: 0.7788 (mm) REVERT: A 782 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7100 (tp30) REVERT: A 784 ARG cc_start: 0.8446 (ptm160) cc_final: 0.7109 (tpt170) REVERT: A 974 LEU cc_start: 0.8541 (mt) cc_final: 0.8189 (mt) REVERT: A 1048 ASP cc_start: 0.9186 (m-30) cc_final: 0.8931 (m-30) REVERT: A 1058 MET cc_start: 0.7718 (mmm) cc_final: 0.6983 (mmt) REVERT: B 161 MET cc_start: 0.7153 (mmm) cc_final: 0.6867 (mtt) REVERT: B 404 VAL cc_start: 0.8670 (t) cc_final: 0.8248 (t) REVERT: B 515 SER cc_start: 0.9357 (p) cc_final: 0.8737 (t) REVERT: B 598 LEU cc_start: 0.9174 (mt) cc_final: 0.8952 (mt) REVERT: B 605 LYS cc_start: 0.8727 (mttt) cc_final: 0.8253 (mttm) REVERT: B 666 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7390 (mm110) REVERT: B 667 GLN cc_start: 0.8241 (pt0) cc_final: 0.8003 (pm20) REVERT: B 693 TRP cc_start: 0.7949 (p-90) cc_final: 0.7279 (p-90) REVERT: B 757 LEU cc_start: 0.8059 (mt) cc_final: 0.7776 (mm) REVERT: B 782 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7085 (tp30) REVERT: B 784 ARG cc_start: 0.8446 (ptm160) cc_final: 0.7017 (tpt170) REVERT: B 851 ASN cc_start: 0.8516 (m-40) cc_final: 0.7795 (m-40) REVERT: B 974 LEU cc_start: 0.8597 (mt) cc_final: 0.8258 (mt) REVERT: B 1048 ASP cc_start: 0.9180 (m-30) cc_final: 0.8929 (m-30) REVERT: B 1058 MET cc_start: 0.7723 (mmm) cc_final: 0.7509 (tpp) REVERT: C 161 MET cc_start: 0.7147 (mmm) cc_final: 0.6865 (mtt) REVERT: C 404 VAL cc_start: 0.8669 (t) cc_final: 0.8243 (t) REVERT: C 515 SER cc_start: 0.9353 (p) cc_final: 0.8726 (t) REVERT: C 598 LEU cc_start: 0.9172 (mt) cc_final: 0.8954 (mt) REVERT: C 605 LYS cc_start: 0.8735 (mttt) cc_final: 0.8250 (mttm) REVERT: C 666 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7376 (mm110) REVERT: C 667 GLN cc_start: 0.8243 (pt0) cc_final: 0.8010 (pm20) REVERT: C 693 TRP cc_start: 0.7953 (p-90) cc_final: 0.7273 (p-90) REVERT: C 757 LEU cc_start: 0.8061 (mt) cc_final: 0.7785 (mm) REVERT: C 782 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7087 (tp30) REVERT: C 784 ARG cc_start: 0.8446 (ptm160) cc_final: 0.7020 (tpt170) REVERT: C 974 LEU cc_start: 0.8566 (mt) cc_final: 0.8219 (mt) REVERT: C 1048 ASP cc_start: 0.9183 (m-30) cc_final: 0.8932 (m-30) REVERT: C 1058 MET cc_start: 0.7713 (mmm) cc_final: 0.7495 (tpp) REVERT: D 161 MET cc_start: 0.7143 (mmm) cc_final: 0.6881 (mtt) REVERT: D 404 VAL cc_start: 0.8668 (t) cc_final: 0.8224 (t) REVERT: D 515 SER cc_start: 0.9354 (p) cc_final: 0.8737 (t) REVERT: D 598 LEU cc_start: 0.9173 (mt) cc_final: 0.8936 (mt) REVERT: D 605 LYS cc_start: 0.8729 (mttt) cc_final: 0.8255 (mttm) REVERT: D 666 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7383 (mm110) REVERT: D 667 GLN cc_start: 0.8241 (pt0) cc_final: 0.8002 (pm20) REVERT: D 693 TRP cc_start: 0.7956 (p-90) cc_final: 0.7277 (p-90) REVERT: D 757 LEU cc_start: 0.8063 (mt) cc_final: 0.7782 (mm) REVERT: D 782 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7088 (tp30) REVERT: D 784 ARG cc_start: 0.8450 (ptm160) cc_final: 0.7021 (tpt170) REVERT: D 851 ASN cc_start: 0.8513 (m-40) cc_final: 0.7792 (m-40) REVERT: D 974 LEU cc_start: 0.8597 (mt) cc_final: 0.8255 (mt) REVERT: D 1048 ASP cc_start: 0.9186 (m-30) cc_final: 0.8936 (m-30) outliers start: 8 outliers final: 0 residues processed: 753 average time/residue: 0.1337 time to fit residues: 165.4575 Evaluate side-chains 508 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 208 ASN A 559 HIS A 572 ASN B 199 ASN B 208 ASN B 559 HIS B 572 ASN B 635 ASN B 851 ASN C 199 ASN C 208 ASN C 559 HIS C 572 ASN C 635 ASN D 199 ASN D 208 ASN D 559 HIS D 572 ASN D 635 ASN D 851 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118940 restraints weight = 49559.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117901 restraints weight = 62328.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118590 restraints weight = 63750.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.118679 restraints weight = 44915.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119715 restraints weight = 39513.785| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23724 Z= 0.223 Angle : 0.655 8.728 32392 Z= 0.346 Chirality : 0.041 0.234 3952 Planarity : 0.004 0.035 3988 Dihedral : 5.174 21.956 3312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.20 % Allowed : 2.76 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2884 helix: 0.16 (0.10), residues: 2196 sheet: -0.33 (0.50), residues: 112 loop : -2.73 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 585 TYR 0.021 0.001 TYR A 772 PHE 0.021 0.002 PHE D 629 TRP 0.019 0.002 TRP A 137 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00507 (23720) covalent geometry : angle 0.65386 (32384) SS BOND : bond 0.00175 ( 4) SS BOND : angle 2.48423 ( 8) hydrogen bonds : bond 0.05107 ( 1602) hydrogen bonds : angle 4.21966 ( 4806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 561 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7640 (mmm) cc_final: 0.7384 (mpp) REVERT: A 521 LEU cc_start: 0.9654 (tp) cc_final: 0.9450 (tp) REVERT: A 598 LEU cc_start: 0.9006 (mt) cc_final: 0.8748 (mt) REVERT: A 605 LYS cc_start: 0.8661 (mttt) cc_final: 0.8271 (mttm) REVERT: A 620 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 624 ARG cc_start: 0.8372 (ttm170) cc_final: 0.8067 (ttm110) REVERT: A 666 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7397 (mm-40) REVERT: A 693 TRP cc_start: 0.7913 (p-90) cc_final: 0.7394 (p-90) REVERT: A 772 TYR cc_start: 0.7567 (m-80) cc_final: 0.7345 (m-80) REVERT: A 782 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7307 (tp30) REVERT: A 784 ARG cc_start: 0.8720 (ptm160) cc_final: 0.7204 (tpt170) REVERT: A 851 ASN cc_start: 0.8685 (m-40) cc_final: 0.8025 (m-40) REVERT: A 852 LEU cc_start: 0.7869 (mt) cc_final: 0.7384 (pt) REVERT: A 974 LEU cc_start: 0.8633 (mt) cc_final: 0.8353 (mt) REVERT: A 1048 ASP cc_start: 0.9258 (m-30) cc_final: 0.8955 (m-30) REVERT: A 1058 MET cc_start: 0.8368 (mmm) cc_final: 0.7901 (tpp) REVERT: B 161 MET cc_start: 0.7648 (mmm) cc_final: 0.7402 (mpp) REVERT: B 598 LEU cc_start: 0.9164 (mt) cc_final: 0.8893 (mt) REVERT: B 605 LYS cc_start: 0.8710 (mttt) cc_final: 0.8289 (mttm) REVERT: B 666 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7218 (mm-40) REVERT: B 667 GLN cc_start: 0.8572 (pt0) cc_final: 0.8164 (pm20) REVERT: B 693 TRP cc_start: 0.7958 (p-90) cc_final: 0.7395 (p-90) REVERT: B 782 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7290 (tp30) REVERT: B 784 ARG cc_start: 0.8700 (ptm160) cc_final: 0.7190 (tpt170) REVERT: B 852 LEU cc_start: 0.7829 (mt) cc_final: 0.7379 (pt) REVERT: B 858 MET cc_start: 0.8141 (mmm) cc_final: 0.7852 (mmm) REVERT: B 974 LEU cc_start: 0.8655 (mt) cc_final: 0.8369 (mt) REVERT: B 1048 ASP cc_start: 0.9268 (m-30) cc_final: 0.8990 (m-30) REVERT: C 161 MET cc_start: 0.7651 (mmm) cc_final: 0.7401 (mpp) REVERT: C 598 LEU cc_start: 0.9116 (mt) cc_final: 0.8853 (mt) REVERT: C 605 LYS cc_start: 0.8714 (mttt) cc_final: 0.8297 (mttm) REVERT: C 666 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7238 (mm-40) REVERT: C 667 GLN cc_start: 0.8589 (pt0) cc_final: 0.8171 (pm20) REVERT: C 693 TRP cc_start: 0.7959 (p-90) cc_final: 0.7397 (p-90) REVERT: C 772 TYR cc_start: 0.7567 (m-80) cc_final: 0.7331 (m-80) REVERT: C 782 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7301 (tp30) REVERT: C 784 ARG cc_start: 0.8707 (ptm160) cc_final: 0.7201 (tpt170) REVERT: C 851 ASN cc_start: 0.8691 (m-40) cc_final: 0.8049 (m-40) REVERT: C 852 LEU cc_start: 0.7865 (mt) cc_final: 0.7389 (pt) REVERT: C 974 LEU cc_start: 0.8649 (mt) cc_final: 0.8393 (mt) REVERT: C 1048 ASP cc_start: 0.9255 (m-30) cc_final: 0.8974 (m-30) REVERT: C 1058 MET cc_start: 0.8421 (mmm) cc_final: 0.8140 (mmm) REVERT: D 161 MET cc_start: 0.7665 (mmm) cc_final: 0.7395 (mpp) REVERT: D 598 LEU cc_start: 0.9108 (mt) cc_final: 0.8868 (mt) REVERT: D 605 LYS cc_start: 0.8705 (mttt) cc_final: 0.8288 (mttm) REVERT: D 666 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7236 (mm-40) REVERT: D 667 GLN cc_start: 0.8585 (pt0) cc_final: 0.8174 (pm20) REVERT: D 693 TRP cc_start: 0.7956 (p-90) cc_final: 0.7395 (p-90) REVERT: D 772 TYR cc_start: 0.7564 (m-80) cc_final: 0.7329 (m-80) REVERT: D 782 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7294 (tp30) REVERT: D 784 ARG cc_start: 0.8692 (ptm160) cc_final: 0.7187 (tpt170) REVERT: D 852 LEU cc_start: 0.7812 (mt) cc_final: 0.7364 (pt) REVERT: D 858 MET cc_start: 0.8153 (mmm) cc_final: 0.7855 (mmm) REVERT: D 974 LEU cc_start: 0.8655 (mt) cc_final: 0.8398 (mt) REVERT: D 1048 ASP cc_start: 0.9261 (m-30) cc_final: 0.8996 (m-30) outliers start: 4 outliers final: 0 residues processed: 561 average time/residue: 0.1381 time to fit residues: 126.3246 Evaluate side-chains 467 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 29 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 233 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN A 510 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A 851 ASN B 438 GLN B 510 GLN B 789 ASN B 851 ASN C 438 GLN C 510 GLN C 789 ASN C 851 ASN D 438 GLN D 510 GLN D 675 GLN D 789 ASN D 851 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121985 restraints weight = 48948.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.120922 restraints weight = 56165.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122083 restraints weight = 45731.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122452 restraints weight = 33461.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122684 restraints weight = 31564.059| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23724 Z= 0.106 Angle : 0.493 7.722 32392 Z= 0.259 Chirality : 0.037 0.186 3952 Planarity : 0.003 0.034 3988 Dihedral : 4.405 20.924 3312 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 0.57 (0.15), residues: 2884 helix: 1.14 (0.11), residues: 2168 sheet: 0.44 (0.52), residues: 112 loop : -2.41 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 585 TYR 0.029 0.001 TYR B 772 PHE 0.012 0.001 PHE B 738 TRP 0.024 0.001 TRP C 876 HIS 0.001 0.000 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00229 (23720) covalent geometry : angle 0.49291 (32384) SS BOND : bond 0.00036 ( 4) SS BOND : angle 1.38862 ( 8) hydrogen bonds : bond 0.03514 ( 1602) hydrogen bonds : angle 3.51880 ( 4806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 THR cc_start: 0.8481 (p) cc_final: 0.8255 (p) REVERT: A 387 SER cc_start: 0.8342 (m) cc_final: 0.8100 (p) REVERT: A 453 TRP cc_start: 0.5929 (p90) cc_final: 0.5581 (p90) REVERT: A 605 LYS cc_start: 0.8700 (mttt) cc_final: 0.8215 (mttm) REVERT: A 693 TRP cc_start: 0.7849 (p-90) cc_final: 0.7328 (p-90) REVERT: A 782 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7359 (tp30) REVERT: A 784 ARG cc_start: 0.8634 (ptm160) cc_final: 0.7182 (tpt170) REVERT: A 852 LEU cc_start: 0.7523 (mt) cc_final: 0.6998 (pt) REVERT: A 974 LEU cc_start: 0.8769 (mt) cc_final: 0.8514 (mt) REVERT: A 1048 ASP cc_start: 0.9251 (m-30) cc_final: 0.8989 (m-30) REVERT: B 141 THR cc_start: 0.8488 (p) cc_final: 0.8265 (p) REVERT: B 387 SER cc_start: 0.8356 (m) cc_final: 0.8123 (p) REVERT: B 453 TRP cc_start: 0.5842 (p90) cc_final: 0.5457 (p90) REVERT: B 605 LYS cc_start: 0.8707 (mttt) cc_final: 0.8221 (mttm) REVERT: B 666 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7033 (mm-40) REVERT: B 667 GLN cc_start: 0.8383 (pt0) cc_final: 0.8143 (pm20) REVERT: B 693 TRP cc_start: 0.7820 (p-90) cc_final: 0.7422 (p-90) REVERT: B 776 PHE cc_start: 0.8739 (t80) cc_final: 0.8520 (t80) REVERT: B 782 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7364 (tp30) REVERT: B 784 ARG cc_start: 0.8643 (ptm160) cc_final: 0.7138 (tpt170) REVERT: B 852 LEU cc_start: 0.7538 (mt) cc_final: 0.7076 (pt) REVERT: B 974 LEU cc_start: 0.8674 (mt) cc_final: 0.8469 (mt) REVERT: B 1048 ASP cc_start: 0.9259 (m-30) cc_final: 0.9008 (m-30) REVERT: C 141 THR cc_start: 0.8477 (p) cc_final: 0.8246 (p) REVERT: C 387 SER cc_start: 0.8361 (m) cc_final: 0.8105 (p) REVERT: C 453 TRP cc_start: 0.5853 (p90) cc_final: 0.5456 (p90) REVERT: C 605 LYS cc_start: 0.8707 (mttt) cc_final: 0.8217 (mttm) REVERT: C 666 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7050 (mm-40) REVERT: C 667 GLN cc_start: 0.8401 (pt0) cc_final: 0.8139 (pm20) REVERT: C 693 TRP cc_start: 0.7828 (p-90) cc_final: 0.7417 (p-90) REVERT: C 776 PHE cc_start: 0.8763 (t80) cc_final: 0.8532 (t80) REVERT: C 782 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7373 (tp30) REVERT: C 784 ARG cc_start: 0.8636 (ptm160) cc_final: 0.7135 (tpt170) REVERT: C 852 LEU cc_start: 0.7494 (mt) cc_final: 0.7000 (pt) REVERT: C 1048 ASP cc_start: 0.9256 (m-30) cc_final: 0.8994 (m-30) REVERT: D 141 THR cc_start: 0.8469 (p) cc_final: 0.8225 (p) REVERT: D 387 SER cc_start: 0.8358 (m) cc_final: 0.8122 (p) REVERT: D 453 TRP cc_start: 0.5825 (p90) cc_final: 0.5460 (p90) REVERT: D 605 LYS cc_start: 0.8700 (mttt) cc_final: 0.8196 (mtpt) REVERT: D 666 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7031 (mm-40) REVERT: D 667 GLN cc_start: 0.8366 (pt0) cc_final: 0.8164 (pm20) REVERT: D 693 TRP cc_start: 0.7823 (p-90) cc_final: 0.7417 (p-90) REVERT: D 776 PHE cc_start: 0.8756 (t80) cc_final: 0.8537 (t80) REVERT: D 782 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7362 (tp30) REVERT: D 784 ARG cc_start: 0.8640 (ptm160) cc_final: 0.7143 (tpt170) REVERT: D 850 ARG cc_start: 0.7898 (tpt90) cc_final: 0.7685 (ttt180) REVERT: D 852 LEU cc_start: 0.7524 (mt) cc_final: 0.7045 (pt) REVERT: D 1048 ASP cc_start: 0.9256 (m-30) cc_final: 0.9002 (m-30) outliers start: 0 outliers final: 0 residues processed: 578 average time/residue: 0.1303 time to fit residues: 123.0808 Evaluate side-chains 472 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 179 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 98 optimal weight: 0.0040 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 0.0030 chunk 157 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 overall best weight: 1.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN A 851 ASN B 510 GLN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN D 510 GLN D 635 ASN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120929 restraints weight = 48996.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120404 restraints weight = 57142.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121352 restraints weight = 46715.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121563 restraints weight = 35299.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121736 restraints weight = 33472.112| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23724 Z= 0.116 Angle : 0.509 6.243 32392 Z= 0.265 Chirality : 0.038 0.246 3952 Planarity : 0.003 0.079 3988 Dihedral : 4.221 19.104 3312 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2884 helix: 1.52 (0.11), residues: 2192 sheet: 0.79 (0.53), residues: 108 loop : -2.37 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 850 TYR 0.030 0.001 TYR C 772 PHE 0.018 0.001 PHE A 748 TRP 0.020 0.001 TRP B 178 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00261 (23720) covalent geometry : angle 0.50860 (32384) SS BOND : bond 0.00090 ( 4) SS BOND : angle 1.37368 ( 8) hydrogen bonds : bond 0.03446 ( 1602) hydrogen bonds : angle 3.42050 ( 4806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.9580 (tp) cc_final: 0.9337 (tp) REVERT: A 605 LYS cc_start: 0.8414 (mttt) cc_final: 0.7969 (mtpt) REVERT: A 693 TRP cc_start: 0.7878 (p-90) cc_final: 0.7351 (p-90) REVERT: A 782 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7382 (tp30) REVERT: A 784 ARG cc_start: 0.8595 (ptm160) cc_final: 0.7242 (tpt170) REVERT: A 843 ILE cc_start: 0.9431 (mm) cc_final: 0.9210 (mm) REVERT: A 851 ASN cc_start: 0.8416 (m110) cc_final: 0.7995 (t0) REVERT: A 852 LEU cc_start: 0.7206 (mt) cc_final: 0.6845 (pp) REVERT: A 968 ILE cc_start: 0.9019 (mt) cc_final: 0.8281 (tp) REVERT: A 1048 ASP cc_start: 0.9193 (m-30) cc_final: 0.8955 (m-30) REVERT: B 521 LEU cc_start: 0.9573 (tp) cc_final: 0.9339 (tp) REVERT: B 605 LYS cc_start: 0.8420 (mttt) cc_final: 0.7963 (mtpt) REVERT: B 666 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6921 (mm-40) REVERT: B 776 PHE cc_start: 0.8558 (t80) cc_final: 0.8339 (t80) REVERT: B 782 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7419 (tp30) REVERT: B 784 ARG cc_start: 0.8600 (ptm160) cc_final: 0.7223 (tpt170) REVERT: B 843 ILE cc_start: 0.9398 (mm) cc_final: 0.9187 (mm) REVERT: B 851 ASN cc_start: 0.8582 (m-40) cc_final: 0.7995 (t0) REVERT: B 852 LEU cc_start: 0.7045 (mt) cc_final: 0.6748 (pp) REVERT: B 968 ILE cc_start: 0.8996 (mt) cc_final: 0.8273 (tp) REVERT: B 1048 ASP cc_start: 0.9192 (m-30) cc_final: 0.8920 (m-30) REVERT: C 521 LEU cc_start: 0.9562 (tp) cc_final: 0.9329 (tp) REVERT: C 605 LYS cc_start: 0.8407 (mttt) cc_final: 0.7962 (mtpt) REVERT: C 666 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6958 (mm-40) REVERT: C 782 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7424 (tp30) REVERT: C 784 ARG cc_start: 0.8608 (ptm160) cc_final: 0.7221 (tpt170) REVERT: C 843 ILE cc_start: 0.9365 (mm) cc_final: 0.9148 (mm) REVERT: C 851 ASN cc_start: 0.8392 (m110) cc_final: 0.8047 (t0) REVERT: C 852 LEU cc_start: 0.7217 (mt) cc_final: 0.6836 (pp) REVERT: C 859 LEU cc_start: 0.9034 (mt) cc_final: 0.8631 (mt) REVERT: C 1048 ASP cc_start: 0.9196 (m-30) cc_final: 0.8939 (m-30) REVERT: D 521 LEU cc_start: 0.9561 (tp) cc_final: 0.9338 (tp) REVERT: D 605 LYS cc_start: 0.8408 (mttt) cc_final: 0.7957 (mtpt) REVERT: D 666 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6907 (mm-40) REVERT: D 782 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7422 (tp30) REVERT: D 784 ARG cc_start: 0.8620 (ptm160) cc_final: 0.7232 (tpt170) REVERT: D 843 ILE cc_start: 0.9396 (mm) cc_final: 0.9184 (mm) REVERT: D 851 ASN cc_start: 0.8450 (m110) cc_final: 0.8007 (t0) REVERT: D 852 LEU cc_start: 0.7214 (mt) cc_final: 0.6948 (pt) REVERT: D 1048 ASP cc_start: 0.9228 (m-30) cc_final: 0.8942 (m-30) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1264 time to fit residues: 114.3495 Evaluate side-chains 472 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 189 optimal weight: 0.9980 chunk 314 optimal weight: 0.1980 chunk 272 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 220 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 40.0000 chunk 273 optimal weight: 7.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 851 ASN B 208 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 ASN C 208 ASN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN C 972 ASN D 208 ASN D 635 ASN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114324 restraints weight = 51185.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113131 restraints weight = 45178.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114125 restraints weight = 46963.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114250 restraints weight = 30899.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114538 restraints weight = 29031.621| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23724 Z= 0.187 Angle : 0.597 8.248 32392 Z= 0.309 Chirality : 0.040 0.214 3952 Planarity : 0.004 0.075 3988 Dihedral : 4.455 19.607 3312 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.20 % Allowed : 2.17 % Favored : 97.64 % 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: 1.28 (0.16), residues: 2884 helix: 1.66 (0.11), residues: 2168 sheet: 0.53 (0.49), residues: 108 loop : -2.11 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 850 TYR 0.029 0.001 TYR B 772 PHE 0.024 0.002 PHE C 869 TRP 0.030 0.002 TRP D 876 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00431 (23720) covalent geometry : angle 0.59600 (32384) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.85285 ( 8) hydrogen bonds : bond 0.04224 ( 1602) hydrogen bonds : angle 3.74170 ( 4806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 513 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7851 (tmm) cc_final: 0.7299 (tmm) REVERT: A 521 LEU cc_start: 0.9677 (tp) cc_final: 0.9415 (tp) REVERT: A 598 LEU cc_start: 0.9316 (mt) cc_final: 0.9104 (mt) REVERT: A 605 LYS cc_start: 0.8520 (mttt) cc_final: 0.8029 (mtpt) REVERT: A 620 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 693 TRP cc_start: 0.7884 (p-90) cc_final: 0.7532 (p-90) REVERT: A 776 PHE cc_start: 0.8904 (t80) cc_final: 0.8685 (t80) REVERT: A 782 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7457 (tp30) REVERT: A 852 LEU cc_start: 0.7342 (mt) cc_final: 0.6977 (pp) REVERT: A 877 MET cc_start: 0.7116 (ttt) cc_final: 0.6905 (ttt) REVERT: A 1048 ASP cc_start: 0.9295 (m-30) cc_final: 0.8991 (m-30) REVERT: B 133 MET cc_start: 0.7863 (tmm) cc_final: 0.7309 (tmm) REVERT: B 161 MET cc_start: 0.7747 (mmp) cc_final: 0.7392 (mpp) REVERT: B 521 LEU cc_start: 0.9677 (tp) cc_final: 0.9414 (tp) REVERT: B 598 LEU cc_start: 0.9331 (mt) cc_final: 0.9109 (mt) REVERT: B 605 LYS cc_start: 0.8472 (mttt) cc_final: 0.8010 (mtpt) REVERT: B 620 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 658 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 782 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7469 (tp30) REVERT: B 843 ILE cc_start: 0.9395 (mm) cc_final: 0.9184 (mm) REVERT: B 851 ASN cc_start: 0.8700 (m110) cc_final: 0.8425 (t0) REVERT: B 852 LEU cc_start: 0.7455 (mt) cc_final: 0.7002 (pp) REVERT: B 865 ASP cc_start: 0.9142 (m-30) cc_final: 0.8826 (m-30) REVERT: B 1048 ASP cc_start: 0.9285 (m-30) cc_final: 0.8970 (m-30) REVERT: C 133 MET cc_start: 0.7848 (tmm) cc_final: 0.7301 (tmm) REVERT: C 161 MET cc_start: 0.7720 (mmp) cc_final: 0.7362 (mpp) REVERT: C 521 LEU cc_start: 0.9679 (tp) cc_final: 0.9413 (tp) REVERT: C 598 LEU cc_start: 0.9334 (mt) cc_final: 0.9104 (mt) REVERT: C 605 LYS cc_start: 0.8477 (mttt) cc_final: 0.8029 (mtpt) REVERT: C 620 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 658 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7615 (tm-30) REVERT: C 782 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7488 (tp30) REVERT: C 852 LEU cc_start: 0.7378 (mt) cc_final: 0.7009 (pp) REVERT: C 865 ASP cc_start: 0.8934 (m-30) cc_final: 0.8666 (m-30) REVERT: C 1048 ASP cc_start: 0.9284 (m-30) cc_final: 0.8973 (m-30) REVERT: D 133 MET cc_start: 0.7860 (tmm) cc_final: 0.7304 (tmm) REVERT: D 161 MET cc_start: 0.7709 (mmp) cc_final: 0.7358 (mpp) REVERT: D 521 LEU cc_start: 0.9687 (tp) cc_final: 0.9429 (tp) REVERT: D 605 LYS cc_start: 0.8448 (mttt) cc_final: 0.8002 (mtpt) REVERT: D 658 GLU cc_start: 0.7993 (pp20) cc_final: 0.7657 (pp20) REVERT: D 782 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7491 (tp30) REVERT: D 852 LEU cc_start: 0.7391 (mt) cc_final: 0.7074 (pt) REVERT: D 865 ASP cc_start: 0.9143 (m-30) cc_final: 0.8822 (m-30) REVERT: D 968 ILE cc_start: 0.9132 (mt) cc_final: 0.8461 (tp) REVERT: D 1048 ASP cc_start: 0.9302 (m-30) cc_final: 0.8963 (m-30) outliers start: 4 outliers final: 0 residues processed: 513 average time/residue: 0.1304 time to fit residues: 111.1617 Evaluate side-chains 443 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 218 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 510 GLN A 972 ASN B 208 ASN B 510 GLN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 ASN C 208 ASN C 510 GLN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116146 restraints weight = 50754.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114697 restraints weight = 64052.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115703 restraints weight = 55059.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116050 restraints weight = 39548.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116205 restraints weight = 37074.727| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23724 Z= 0.204 Angle : 0.627 8.294 32392 Z= 0.323 Chirality : 0.041 0.208 3952 Planarity : 0.004 0.035 3988 Dihedral : 4.539 20.878 3312 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.15 % Allowed : 3.00 % Favored : 96.85 % 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: 1.26 (0.16), residues: 2884 helix: 1.64 (0.11), residues: 2168 sheet: 0.56 (0.50), residues: 108 loop : -2.10 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 532 TYR 0.031 0.001 TYR B 772 PHE 0.031 0.002 PHE A 868 TRP 0.035 0.002 TRP C 876 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00473 (23720) covalent geometry : angle 0.62600 (32384) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.86995 ( 8) hydrogen bonds : bond 0.04390 ( 1602) hydrogen bonds : angle 3.88160 ( 4806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 502 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.9680 (tp) cc_final: 0.9441 (tp) REVERT: A 605 LYS cc_start: 0.8397 (mttt) cc_final: 0.8000 (mtpt) REVERT: A 693 TRP cc_start: 0.7930 (p-90) cc_final: 0.7433 (p-90) REVERT: A 782 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7407 (tp30) REVERT: A 851 ASN cc_start: 0.8665 (m-40) cc_final: 0.8441 (t0) REVERT: A 852 LEU cc_start: 0.7392 (mt) cc_final: 0.6991 (pp) REVERT: A 877 MET cc_start: 0.7313 (ttt) cc_final: 0.7039 (ttt) REVERT: A 968 ILE cc_start: 0.9047 (mt) cc_final: 0.8364 (tp) REVERT: A 1048 ASP cc_start: 0.9297 (m-30) cc_final: 0.8981 (m-30) REVERT: B 521 LEU cc_start: 0.9675 (tp) cc_final: 0.9428 (tp) REVERT: B 605 LYS cc_start: 0.8396 (mttt) cc_final: 0.7994 (mtpt) REVERT: B 782 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7421 (tp30) REVERT: B 852 LEU cc_start: 0.7358 (mt) cc_final: 0.6965 (pp) REVERT: B 1048 ASP cc_start: 0.9249 (m-30) cc_final: 0.8920 (m-30) REVERT: C 521 LEU cc_start: 0.9674 (tp) cc_final: 0.9441 (tp) REVERT: C 605 LYS cc_start: 0.8403 (mttt) cc_final: 0.8005 (mtpt) REVERT: C 776 PHE cc_start: 0.8805 (t80) cc_final: 0.8590 (t80) REVERT: C 782 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7432 (tp30) REVERT: C 843 ILE cc_start: 0.9391 (mm) cc_final: 0.9172 (mm) REVERT: C 851 ASN cc_start: 0.8739 (m-40) cc_final: 0.8482 (t0) REVERT: C 852 LEU cc_start: 0.7428 (mt) cc_final: 0.6946 (pp) REVERT: C 865 ASP cc_start: 0.8877 (m-30) cc_final: 0.8612 (m-30) REVERT: C 1048 ASP cc_start: 0.9273 (m-30) cc_final: 0.8954 (m-30) REVERT: D 521 LEU cc_start: 0.9685 (tp) cc_final: 0.9451 (tp) REVERT: D 605 LYS cc_start: 0.8384 (mttt) cc_final: 0.7986 (mtpt) REVERT: D 782 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7427 (tp30) REVERT: D 801 MET cc_start: 0.8968 (tpp) cc_final: 0.8727 (tpp) REVERT: D 843 ILE cc_start: 0.9390 (mm) cc_final: 0.9180 (mm) REVERT: D 852 LEU cc_start: 0.7475 (mt) cc_final: 0.7095 (pt) REVERT: D 865 ASP cc_start: 0.9047 (m-30) cc_final: 0.8761 (m-30) REVERT: D 968 ILE cc_start: 0.9068 (mt) cc_final: 0.8408 (tp) REVERT: D 1048 ASP cc_start: 0.9309 (m-30) cc_final: 0.8987 (m-30) outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.1312 time to fit residues: 111.0146 Evaluate side-chains 425 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 128 optimal weight: 0.5980 chunk 310 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 319 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 256 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 ASN C 208 ASN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN D 635 ASN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115097 restraints weight = 51217.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114150 restraints weight = 56196.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115049 restraints weight = 46999.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115278 restraints weight = 35842.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115426 restraints weight = 33645.580| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23724 Z= 0.172 Angle : 0.599 8.605 32392 Z= 0.305 Chirality : 0.040 0.188 3952 Planarity : 0.003 0.036 3988 Dihedral : 4.366 19.201 3312 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % 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: 1.48 (0.16), residues: 2884 helix: 1.81 (0.11), residues: 2168 sheet: 0.43 (0.48), residues: 108 loop : -2.05 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 624 TYR 0.010 0.001 TYR B 835 PHE 0.026 0.002 PHE C 869 TRP 0.036 0.002 TRP B 876 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00397 (23720) covalent geometry : angle 0.59812 (32384) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.56853 ( 8) hydrogen bonds : bond 0.04088 ( 1602) hydrogen bonds : angle 3.70534 ( 4806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 504 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7744 (tmm) cc_final: 0.7096 (tmm) REVERT: A 521 LEU cc_start: 0.9661 (tp) cc_final: 0.9426 (tp) REVERT: A 598 LEU cc_start: 0.9387 (mt) cc_final: 0.9110 (mt) REVERT: A 605 LYS cc_start: 0.8363 (mttt) cc_final: 0.8053 (mtpt) REVERT: A 693 TRP cc_start: 0.7843 (p-90) cc_final: 0.7394 (p-90) REVERT: A 782 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 851 ASN cc_start: 0.8767 (m-40) cc_final: 0.8484 (t0) REVERT: A 852 LEU cc_start: 0.7375 (mt) cc_final: 0.6950 (pp) REVERT: A 865 ASP cc_start: 0.9081 (m-30) cc_final: 0.8796 (m-30) REVERT: A 1048 ASP cc_start: 0.9252 (m-30) cc_final: 0.8928 (m-30) REVERT: B 133 MET cc_start: 0.7775 (tmm) cc_final: 0.7113 (tmm) REVERT: B 161 MET cc_start: 0.7701 (mmp) cc_final: 0.7048 (mmt) REVERT: B 521 LEU cc_start: 0.9655 (tp) cc_final: 0.9419 (tp) REVERT: B 598 LEU cc_start: 0.9393 (mt) cc_final: 0.9105 (mt) REVERT: B 605 LYS cc_start: 0.8344 (mttt) cc_final: 0.8038 (mtpt) REVERT: B 693 TRP cc_start: 0.7784 (p-90) cc_final: 0.7414 (p-90) REVERT: B 782 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7457 (tp30) REVERT: B 843 ILE cc_start: 0.9385 (mm) cc_final: 0.9170 (mm) REVERT: B 852 LEU cc_start: 0.7483 (mt) cc_final: 0.6906 (pp) REVERT: B 1048 ASP cc_start: 0.9244 (m-30) cc_final: 0.8909 (m-30) REVERT: C 133 MET cc_start: 0.7772 (tmm) cc_final: 0.7115 (tmm) REVERT: C 161 MET cc_start: 0.7669 (mmp) cc_final: 0.7021 (mmt) REVERT: C 521 LEU cc_start: 0.9659 (tp) cc_final: 0.9427 (tp) REVERT: C 598 LEU cc_start: 0.9376 (mt) cc_final: 0.9086 (mt) REVERT: C 605 LYS cc_start: 0.8358 (mttt) cc_final: 0.8054 (mtpt) REVERT: C 693 TRP cc_start: 0.7781 (p-90) cc_final: 0.7406 (p-90) REVERT: C 776 PHE cc_start: 0.8799 (t80) cc_final: 0.8552 (t80) REVERT: C 782 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7461 (tp30) REVERT: C 843 ILE cc_start: 0.9385 (mm) cc_final: 0.9177 (mm) REVERT: C 852 LEU cc_start: 0.7398 (mt) cc_final: 0.6986 (pp) REVERT: C 865 ASP cc_start: 0.8882 (m-30) cc_final: 0.8637 (m-30) REVERT: C 1048 ASP cc_start: 0.9250 (m-30) cc_final: 0.8914 (m-30) REVERT: D 133 MET cc_start: 0.7790 (tmm) cc_final: 0.7129 (tmm) REVERT: D 161 MET cc_start: 0.7665 (mmp) cc_final: 0.7020 (mmt) REVERT: D 521 LEU cc_start: 0.9655 (tp) cc_final: 0.9425 (tp) REVERT: D 598 LEU cc_start: 0.9369 (mt) cc_final: 0.9169 (mt) REVERT: D 605 LYS cc_start: 0.8325 (mttt) cc_final: 0.8026 (mtpt) REVERT: D 658 GLU cc_start: 0.8301 (pp20) cc_final: 0.7700 (pp20) REVERT: D 693 TRP cc_start: 0.7777 (p-90) cc_final: 0.7407 (p-90) REVERT: D 776 PHE cc_start: 0.8797 (t80) cc_final: 0.8574 (t80) REVERT: D 782 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7468 (tp30) REVERT: D 852 LEU cc_start: 0.7488 (mt) cc_final: 0.7078 (pt) REVERT: D 865 ASP cc_start: 0.8988 (m-30) cc_final: 0.8702 (m-30) REVERT: D 968 ILE cc_start: 0.9117 (mt) cc_final: 0.8437 (tp) REVERT: D 1048 ASP cc_start: 0.9272 (m-30) cc_final: 0.8910 (m-30) outliers start: 2 outliers final: 0 residues processed: 504 average time/residue: 0.1185 time to fit residues: 101.6336 Evaluate side-chains 427 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 216 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 231 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 158 optimal weight: 40.0000 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.140409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115577 restraints weight = 50221.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.116611 restraints weight = 44872.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117687 restraints weight = 31746.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117487 restraints weight = 26234.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117658 restraints weight = 25707.110| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23724 Z= 0.135 Angle : 0.562 8.689 32392 Z= 0.287 Chirality : 0.039 0.178 3952 Planarity : 0.003 0.035 3988 Dihedral : 4.259 26.498 3312 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.16), residues: 2884 helix: 1.94 (0.11), residues: 2168 sheet: 0.85 (0.49), residues: 108 loop : -2.05 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 850 TYR 0.030 0.001 TYR A 772 PHE 0.028 0.001 PHE C 869 TRP 0.034 0.001 TRP B 876 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00308 (23720) covalent geometry : angle 0.56166 (32384) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.52277 ( 8) hydrogen bonds : bond 0.03709 ( 1602) hydrogen bonds : angle 3.57870 ( 4806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 493 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.7832 (tmm) cc_final: 0.7193 (tmm) REVERT: A 521 LEU cc_start: 0.9646 (tp) cc_final: 0.9407 (tp) REVERT: A 605 LYS cc_start: 0.8312 (mttt) cc_final: 0.7981 (mtpt) REVERT: A 693 TRP cc_start: 0.7817 (p-90) cc_final: 0.7416 (p-90) REVERT: A 782 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7434 (tp30) REVERT: A 801 MET cc_start: 0.8948 (tpp) cc_final: 0.8351 (ttp) REVERT: A 843 ILE cc_start: 0.9412 (mm) cc_final: 0.9181 (mm) REVERT: A 851 ASN cc_start: 0.8598 (m110) cc_final: 0.8327 (t0) REVERT: A 852 LEU cc_start: 0.7303 (mt) cc_final: 0.6934 (pp) REVERT: A 865 ASP cc_start: 0.9102 (m-30) cc_final: 0.8797 (m-30) REVERT: A 1048 ASP cc_start: 0.9202 (m-30) cc_final: 0.8864 (m-30) REVERT: B 133 MET cc_start: 0.7824 (tmm) cc_final: 0.7193 (tmm) REVERT: B 161 MET cc_start: 0.7739 (mmp) cc_final: 0.7113 (mmt) REVERT: B 521 LEU cc_start: 0.9646 (tp) cc_final: 0.9408 (tp) REVERT: B 605 LYS cc_start: 0.8321 (mttt) cc_final: 0.7967 (mtpt) REVERT: B 693 TRP cc_start: 0.7811 (p-90) cc_final: 0.7531 (p-90) REVERT: B 697 LEU cc_start: 0.8174 (mt) cc_final: 0.7974 (pp) REVERT: B 782 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7450 (tp30) REVERT: B 801 MET cc_start: 0.8943 (tpp) cc_final: 0.8343 (ttp) REVERT: B 865 ASP cc_start: 0.9055 (m-30) cc_final: 0.8647 (m-30) REVERT: B 1048 ASP cc_start: 0.9173 (m-30) cc_final: 0.8852 (m-30) REVERT: C 133 MET cc_start: 0.7818 (tmm) cc_final: 0.7189 (tmm) REVERT: C 161 MET cc_start: 0.7735 (mmp) cc_final: 0.7105 (mmt) REVERT: C 521 LEU cc_start: 0.9643 (tp) cc_final: 0.9401 (tp) REVERT: C 605 LYS cc_start: 0.8375 (mttt) cc_final: 0.7994 (mtpt) REVERT: C 693 TRP cc_start: 0.7772 (p-90) cc_final: 0.7304 (p-90) REVERT: C 776 PHE cc_start: 0.8853 (t80) cc_final: 0.8593 (t80) REVERT: C 782 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7470 (tp30) REVERT: C 784 ARG cc_start: 0.8736 (ptm160) cc_final: 0.7229 (tpt170) REVERT: C 801 MET cc_start: 0.8931 (tpp) cc_final: 0.8355 (ttp) REVERT: C 852 LEU cc_start: 0.7219 (mt) cc_final: 0.6890 (pt) REVERT: C 865 ASP cc_start: 0.8904 (m-30) cc_final: 0.8625 (m-30) REVERT: C 1048 ASP cc_start: 0.9196 (m-30) cc_final: 0.8868 (m-30) REVERT: D 133 MET cc_start: 0.7823 (tmm) cc_final: 0.7205 (tmm) REVERT: D 161 MET cc_start: 0.7720 (mmp) cc_final: 0.7098 (mmt) REVERT: D 521 LEU cc_start: 0.9652 (tp) cc_final: 0.9408 (tp) REVERT: D 605 LYS cc_start: 0.8342 (mttt) cc_final: 0.7975 (mtpt) REVERT: D 658 GLU cc_start: 0.8222 (pp20) cc_final: 0.7699 (pp20) REVERT: D 693 TRP cc_start: 0.7703 (p-90) cc_final: 0.7381 (p-90) REVERT: D 782 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7454 (tp30) REVERT: D 852 LEU cc_start: 0.7433 (mt) cc_final: 0.7099 (pt) REVERT: D 856 ILE cc_start: 0.7908 (mt) cc_final: 0.7656 (mt) REVERT: D 865 ASP cc_start: 0.9109 (m-30) cc_final: 0.8834 (m-30) REVERT: D 1048 ASP cc_start: 0.9232 (m-30) cc_final: 0.8769 (m-30) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.1234 time to fit residues: 102.0267 Evaluate side-chains 417 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 155 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 chunk 312 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS A 851 ASN B 259 HIS ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 ASN C 259 HIS ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.137162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115836 restraints weight = 50652.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114201 restraints weight = 50459.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115344 restraints weight = 52257.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115310 restraints weight = 36334.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115566 restraints weight = 34330.924| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23724 Z= 0.218 Angle : 0.663 8.486 32392 Z= 0.340 Chirality : 0.042 0.286 3952 Planarity : 0.004 0.035 3988 Dihedral : 4.593 27.437 3312 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 1.33 (0.16), residues: 2884 helix: 1.70 (0.11), residues: 2196 sheet: 0.70 (0.50), residues: 108 loop : -2.34 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 850 TYR 0.026 0.002 TYR B 772 PHE 0.020 0.002 PHE D 629 TRP 0.041 0.002 TRP B 876 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00501 (23720) covalent geometry : angle 0.66177 (32384) SS BOND : bond 0.00310 ( 4) SS BOND : angle 2.43465 ( 8) hydrogen bonds : bond 0.04601 ( 1602) hydrogen bonds : angle 4.01520 ( 4806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.9703 (tp) cc_final: 0.9472 (tp) REVERT: A 605 LYS cc_start: 0.8366 (mttt) cc_final: 0.8036 (mtpt) REVERT: A 693 TRP cc_start: 0.7909 (p-90) cc_final: 0.7411 (p-90) REVERT: A 776 PHE cc_start: 0.8837 (t80) cc_final: 0.8578 (t80) REVERT: A 782 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7398 (tp30) REVERT: A 843 ILE cc_start: 0.9397 (mm) cc_final: 0.9187 (mm) REVERT: A 852 LEU cc_start: 0.7693 (mt) cc_final: 0.7146 (pp) REVERT: A 865 ASP cc_start: 0.9064 (m-30) cc_final: 0.8754 (m-30) REVERT: A 968 ILE cc_start: 0.9093 (mt) cc_final: 0.8422 (tp) REVERT: A 1048 ASP cc_start: 0.9278 (m-30) cc_final: 0.8828 (m-30) REVERT: B 161 MET cc_start: 0.7834 (mmp) cc_final: 0.7250 (mmt) REVERT: B 521 LEU cc_start: 0.9691 (tp) cc_final: 0.9460 (tp) REVERT: B 605 LYS cc_start: 0.8370 (mttt) cc_final: 0.8038 (mtpt) REVERT: B 693 TRP cc_start: 0.7868 (p-90) cc_final: 0.7408 (p-90) REVERT: B 782 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7476 (tp30) REVERT: B 843 ILE cc_start: 0.9340 (mm) cc_final: 0.9130 (mm) REVERT: B 865 ASP cc_start: 0.9011 (m-30) cc_final: 0.8677 (m-30) REVERT: B 1048 ASP cc_start: 0.9237 (m-30) cc_final: 0.8759 (m-30) REVERT: C 161 MET cc_start: 0.7862 (mmp) cc_final: 0.7257 (mmt) REVERT: C 521 LEU cc_start: 0.9695 (tp) cc_final: 0.9459 (tp) REVERT: C 605 LYS cc_start: 0.8363 (mttt) cc_final: 0.8036 (mtpt) REVERT: C 693 TRP cc_start: 0.7850 (p-90) cc_final: 0.7437 (p-90) REVERT: C 776 PHE cc_start: 0.8774 (t80) cc_final: 0.8538 (t80) REVERT: C 782 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7414 (tp30) REVERT: C 843 ILE cc_start: 0.9386 (mm) cc_final: 0.9178 (mm) REVERT: C 852 LEU cc_start: 0.7429 (mt) cc_final: 0.6903 (pp) REVERT: C 865 ASP cc_start: 0.8927 (m-30) cc_final: 0.8662 (m-30) REVERT: C 968 ILE cc_start: 0.9100 (mt) cc_final: 0.8459 (tp) REVERT: C 1048 ASP cc_start: 0.9267 (m-30) cc_final: 0.8814 (m-30) REVERT: D 161 MET cc_start: 0.7835 (mmp) cc_final: 0.7263 (mmt) REVERT: D 521 LEU cc_start: 0.9703 (tp) cc_final: 0.9459 (tp) REVERT: D 605 LYS cc_start: 0.8380 (mttt) cc_final: 0.8035 (mtpt) REVERT: D 693 TRP cc_start: 0.7852 (p-90) cc_final: 0.7444 (p-90) REVERT: D 776 PHE cc_start: 0.8816 (t80) cc_final: 0.8610 (t80) REVERT: D 782 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7440 (tp30) REVERT: D 852 LEU cc_start: 0.7468 (mt) cc_final: 0.6980 (pt) REVERT: D 865 ASP cc_start: 0.9061 (m-30) cc_final: 0.8765 (m-30) REVERT: D 968 ILE cc_start: 0.9113 (mt) cc_final: 0.8472 (tp) REVERT: D 1048 ASP cc_start: 0.9260 (m-30) cc_final: 0.8866 (m-30) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1219 time to fit residues: 103.8463 Evaluate side-chains 414 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 215 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 185 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 198 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 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 = 0.3778 r_free = 0.3778 target = 0.142855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119404 restraints weight = 50381.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118707 restraints weight = 48881.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119679 restraints weight = 43061.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119874 restraints weight = 31849.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120020 restraints weight = 31624.829| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23724 Z= 0.108 Angle : 0.545 9.455 32392 Z= 0.280 Chirality : 0.038 0.220 3952 Planarity : 0.003 0.038 3988 Dihedral : 4.098 26.637 3312 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 2884 helix: 2.16 (0.11), residues: 2188 sheet: 1.31 (0.50), residues: 108 loop : -2.11 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 850 TYR 0.018 0.001 TYR D 186 PHE 0.025 0.001 PHE D 738 TRP 0.029 0.001 TRP B 876 HIS 0.001 0.000 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00237 (23720) covalent geometry : angle 0.54475 (32384) SS BOND : bond 0.00045 ( 4) SS BOND : angle 1.45692 ( 8) hydrogen bonds : bond 0.03169 ( 1602) hydrogen bonds : angle 3.44108 ( 4806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 LEU cc_start: 0.9604 (tp) cc_final: 0.9403 (tp) REVERT: A 605 LYS cc_start: 0.8353 (mttt) cc_final: 0.7943 (mtpt) REVERT: A 693 TRP cc_start: 0.7741 (p-90) cc_final: 0.7306 (p-90) REVERT: A 782 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7368 (tp30) REVERT: A 784 ARG cc_start: 0.8678 (ptm160) cc_final: 0.7240 (tpt170) REVERT: A 801 MET cc_start: 0.8839 (tpp) cc_final: 0.8412 (ttp) REVERT: A 851 ASN cc_start: 0.8710 (m110) cc_final: 0.8296 (t0) REVERT: A 852 LEU cc_start: 0.7344 (mt) cc_final: 0.7090 (pt) REVERT: A 968 ILE cc_start: 0.9002 (mt) cc_final: 0.8381 (tp) REVERT: A 1048 ASP cc_start: 0.9222 (m-30) cc_final: 0.8891 (m-30) REVERT: B 161 MET cc_start: 0.7719 (mmp) cc_final: 0.7218 (mmt) REVERT: B 521 LEU cc_start: 0.9598 (tp) cc_final: 0.9393 (tp) REVERT: B 605 LYS cc_start: 0.8368 (mttt) cc_final: 0.7968 (mtpt) REVERT: B 693 TRP cc_start: 0.7796 (p-90) cc_final: 0.7479 (p-90) REVERT: B 782 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7410 (tp30) REVERT: B 784 ARG cc_start: 0.8667 (ptm160) cc_final: 0.7252 (tpt170) REVERT: B 801 MET cc_start: 0.8861 (tpp) cc_final: 0.8391 (ttp) REVERT: B 968 ILE cc_start: 0.9051 (mt) cc_final: 0.8379 (tp) REVERT: B 1048 ASP cc_start: 0.9196 (m-30) cc_final: 0.8855 (m-30) REVERT: C 161 MET cc_start: 0.7722 (mmp) cc_final: 0.7193 (mmt) REVERT: C 521 LEU cc_start: 0.9601 (tp) cc_final: 0.9396 (tp) REVERT: C 605 LYS cc_start: 0.8341 (mttt) cc_final: 0.7951 (mtpt) REVERT: C 693 TRP cc_start: 0.7768 (p-90) cc_final: 0.7493 (p-90) REVERT: C 697 LEU cc_start: 0.8212 (mt) cc_final: 0.7991 (pp) REVERT: C 782 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7375 (tp30) REVERT: C 784 ARG cc_start: 0.8678 (ptm160) cc_final: 0.7255 (tpt170) REVERT: C 801 MET cc_start: 0.8825 (tpp) cc_final: 0.8407 (ttp) REVERT: C 865 ASP cc_start: 0.9025 (m-30) cc_final: 0.8798 (m-30) REVERT: C 968 ILE cc_start: 0.9072 (mt) cc_final: 0.8424 (tp) REVERT: C 1048 ASP cc_start: 0.9215 (m-30) cc_final: 0.8882 (m-30) REVERT: D 521 LEU cc_start: 0.9618 (tp) cc_final: 0.9376 (tp) REVERT: D 605 LYS cc_start: 0.8364 (mttt) cc_final: 0.7952 (mtpt) REVERT: D 658 GLU cc_start: 0.8184 (pp20) cc_final: 0.7715 (pp20) REVERT: D 693 TRP cc_start: 0.7725 (p-90) cc_final: 0.7384 (p-90) REVERT: D 782 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7371 (tp30) REVERT: D 784 ARG cc_start: 0.8688 (ptm160) cc_final: 0.7272 (tpt170) REVERT: D 852 LEU cc_start: 0.7398 (mt) cc_final: 0.7133 (pt) REVERT: D 968 ILE cc_start: 0.9031 (mt) cc_final: 0.8388 (tp) REVERT: D 993 TRP cc_start: 0.8095 (t60) cc_final: 0.7867 (t60) REVERT: D 1048 ASP cc_start: 0.9206 (m-30) cc_final: 0.8684 (m-30) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.1312 time to fit residues: 109.9142 Evaluate side-chains 408 residues out of total 2764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 92 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 204 optimal weight: 0.0470 chunk 146 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 147 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 6.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 851 ASN B 438 GLN B 480 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN C 480 ASN ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 480 ASN D 675 GLN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113681 restraints weight = 51113.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112052 restraints weight = 59104.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112945 restraints weight = 56779.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113320 restraints weight = 40383.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113473 restraints weight = 38464.211| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 23724 Z= 0.288 Angle : 0.739 10.097 32392 Z= 0.381 Chirality : 0.044 0.238 3952 Planarity : 0.004 0.036 3988 Dihedral : 4.745 27.444 3312 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.15 % Allowed : 0.79 % Favored : 99.06 % 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: 1.24 (0.16), residues: 2884 helix: 1.62 (0.11), residues: 2188 sheet: 0.94 (0.51), residues: 108 loop : -2.33 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 850 TYR 0.034 0.002 TYR C 980 PHE 0.023 0.002 PHE D 629 TRP 0.045 0.003 TRP B 876 HIS 0.008 0.002 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00660 (23720) covalent geometry : angle 0.73861 (32384) SS BOND : bond 0.00082 ( 4) SS BOND : angle 2.40778 ( 8) hydrogen bonds : bond 0.05055 ( 1602) hydrogen bonds : angle 4.30825 ( 4806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.42 seconds wall clock time: 58 minutes 54.37 seconds (3534.37 seconds total)