Starting phenix.real_space_refine (version: dev) on Thu Dec 15 00:37:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr4_0489/12_2022/6nr4_0489_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr4_0489/12_2022/6nr4_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr4_0489/12_2022/6nr4_0489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr4_0489/12_2022/6nr4_0489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr4_0489/12_2022/6nr4_0489_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nr4_0489/12_2022/6nr4_0489_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 23264 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 5816 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 18, 'TRANS': 785} Chain breaks: 21 Unresolved non-hydrogen bonds: 810 Unresolved non-hydrogen angles: 1036 Unresolved non-hydrogen dihedrals: 651 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 7, 'UNK:plan-1': 45, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 491 Chain: "B" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 5816 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 18, 'TRANS': 785} Chain breaks: 21 Unresolved non-hydrogen bonds: 810 Unresolved non-hydrogen angles: 1036 Unresolved non-hydrogen dihedrals: 651 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 7, 'UNK:plan-1': 45, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 491 Chain: "C" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 5816 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 18, 'TRANS': 785} Chain breaks: 21 Unresolved non-hydrogen bonds: 810 Unresolved non-hydrogen angles: 1036 Unresolved non-hydrogen dihedrals: 651 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 7, 'UNK:plan-1': 45, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 491 Chain: "D" Number of atoms: 5816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 5816 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 228} Link IDs: {'PTRANS': 18, 'TRANS': 785} Chain breaks: 21 Unresolved non-hydrogen bonds: 810 Unresolved non-hydrogen angles: 1036 Unresolved non-hydrogen dihedrals: 651 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'ASN:plan1': 8, 'TYR:plan': 7, 'UNK:plan-1': 45, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 491 Time building chain proxies: 13.57, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 9.90 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 1.26 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: 8.47 Time building geometry restraints manager: 10.57 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: 98.92 - 105.95: 324 105.95 - 112.98: 13139 112.98 - 120.00: 7654 120.00 - 127.03: 10996 127.03 - 134.05: 271 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 2.440 nonbonded pdb=" O LEU D 592 " pdb=" OG SER D 595 " model vdw 2.319 2.440 nonbonded pdb=" O LEU B 592 " pdb=" OG SER B 595 " model vdw 2.319 2.440 nonbonded pdb=" O LEU C 592 " pdb=" OG SER C 595 " model vdw 2.319 2.440 nonbonded pdb=" OG SER C 409 " pdb=" NE2 GLN C 438 " model vdw 2.362 2.520 ... (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 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.890 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.190 Process input model: 61.290 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 23720 Z= 0.384 Angle : 0.934 10.614 32384 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (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 *********************** 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 fitting. rotamer outliers: 8 poor density : 745 time to evaluate : 2.740 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 outliers start: 8 outliers final: 0 residues processed: 753 average time/residue: 0.2901 time to fit residues: 352.9865 Evaluate side-chains 497 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 2.482 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.9990 chunk 242 optimal weight: 40.0000 chunk 134 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 97 optimal weight: 0.0030 chunk 152 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS A 572 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 GLN A 675 GLN A 851 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 HIS B 572 ASN B 635 ASN B 666 GLN B 675 GLN B 851 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 HIS C 572 ASN C 635 ASN C 666 GLN C 675 GLN C 851 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 HIS D 572 ASN D 635 ASN D 666 GLN D 675 GLN D 851 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23720 Z= 0.166 Angle : 0.524 5.965 32384 Z= 0.277 Chirality : 0.038 0.229 3952 Planarity : 0.003 0.035 3988 Dihedral : 4.768 20.236 3312 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 2884 helix: 0.34 (0.10), residues: 2168 sheet: 0.12 (0.50), residues: 112 loop : -2.71 (0.21), residues: 604 *********************** 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 592 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 592 time to evaluate : 2.457 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 outliers start: 0 outliers final: 0 residues processed: 592 average time/residue: 0.3067 time to fit residues: 293.4487 Evaluate side-chains 478 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 197 optimal weight: 0.0770 chunk 80 optimal weight: 30.0000 chunk 291 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 259 optimal weight: 0.0370 chunk 288 optimal weight: 10.0000 chunk 99 optimal weight: 0.0870 chunk 233 optimal weight: 8.9990 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 ASN C 199 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 851 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 23720 Z= 0.186 Angle : 0.523 6.957 32384 Z= 0.272 Chirality : 0.038 0.176 3952 Planarity : 0.003 0.033 3988 Dihedral : 4.462 21.488 3312 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2884 helix: 1.19 (0.11), residues: 2184 sheet: 0.71 (0.52), residues: 112 loop : -2.34 (0.24), residues: 588 *********************** 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 563 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 563 average time/residue: 0.2986 time to fit residues: 272.1076 Evaluate side-chains 472 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23720 Z= 0.212 Angle : 0.533 6.763 32384 Z= 0.276 Chirality : 0.039 0.222 3952 Planarity : 0.003 0.035 3988 Dihedral : 4.422 24.865 3312 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2884 helix: 1.68 (0.11), residues: 2164 sheet: 1.02 (0.53), residues: 108 loop : -2.22 (0.24), residues: 612 *********************** 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 491 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.2986 time to fit residues: 243.4183 Evaluate side-chains 406 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 277 optimal weight: 0.0770 chunk 78 optimal weight: 40.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23720 Z= 0.237 Angle : 0.558 7.270 32384 Z= 0.288 Chirality : 0.039 0.195 3952 Planarity : 0.003 0.034 3988 Dihedral : 4.387 22.504 3312 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2884 helix: 1.83 (0.11), residues: 2160 sheet: 0.90 (0.51), residues: 108 loop : -2.10 (0.25), residues: 616 *********************** 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 490 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.604 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 outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3033 time to fit residues: 239.7731 Evaluate side-chains 395 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 20.0000 chunk 278 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 309 optimal weight: 5.9990 chunk 257 optimal weight: 0.0670 chunk 143 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 162 optimal weight: 40.0000 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 741 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN B 741 ASN C 199 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 ASN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN D 635 ASN ** D 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 23720 Z= 0.134 Angle : 0.488 6.668 32384 Z= 0.249 Chirality : 0.037 0.171 3952 Planarity : 0.003 0.034 3988 Dihedral : 4.060 24.600 3312 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.16), residues: 2884 helix: 2.19 (0.11), residues: 2164 sheet: 1.55 (0.51), residues: 108 loop : -2.07 (0.24), residues: 612 *********************** 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 519 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.3021 time to fit residues: 255.2341 Evaluate side-chains 421 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 2.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 308 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 23720 Z= 0.169 Angle : 0.533 9.490 32384 Z= 0.268 Chirality : 0.038 0.159 3952 Planarity : 0.003 0.034 3988 Dihedral : 4.036 24.806 3312 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.16), residues: 2884 helix: 2.27 (0.11), residues: 2168 sheet: 1.84 (0.51), residues: 108 loop : -1.94 (0.25), residues: 608 *********************** 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 496 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.2969 time to fit residues: 243.0724 Evaluate side-chains 409 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 210 optimal weight: 0.1980 chunk 152 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 242 optimal weight: 40.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 972 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23720 Z= 0.227 Angle : 0.567 8.045 32384 Z= 0.287 Chirality : 0.039 0.222 3952 Planarity : 0.003 0.032 3988 Dihedral : 4.181 26.809 3312 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.16), residues: 2884 helix: 2.26 (0.11), residues: 2164 sheet: 1.84 (0.60), residues: 68 loop : -1.76 (0.25), residues: 652 *********************** 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 485 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.3024 time to fit residues: 238.6409 Evaluate side-chains 384 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 287 optimal weight: 0.9990 chunk 172 optimal weight: 30.0000 chunk 125 optimal weight: 0.2980 chunk 225 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23720 Z= 0.183 Angle : 0.541 7.350 32384 Z= 0.273 Chirality : 0.038 0.164 3952 Planarity : 0.003 0.033 3988 Dihedral : 4.094 27.034 3312 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2884 helix: 2.32 (0.11), residues: 2196 sheet: 1.92 (0.59), residues: 68 loop : -1.98 (0.24), residues: 620 *********************** 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 477 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2906 time to fit residues: 228.3472 Evaluate side-chains 388 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 3.9990 chunk 303 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 318 optimal weight: 40.0000 chunk 293 optimal weight: 8.9990 chunk 253 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23720 Z= 0.176 Angle : 0.539 7.753 32384 Z= 0.271 Chirality : 0.038 0.180 3952 Planarity : 0.003 0.033 3988 Dihedral : 4.055 27.303 3312 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.16), residues: 2884 helix: 2.34 (0.11), residues: 2196 sheet: 2.01 (0.52), residues: 108 loop : -2.14 (0.25), residues: 580 ********************** 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 460 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.2906 time to fit residues: 221.4782 Evaluate side-chains 378 residues out of total 2764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 9.9990 chunk 270 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 70 optimal weight: 9.9990 chunk 254 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122808 restraints weight = 49377.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123695 restraints weight = 47812.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123021 restraints weight = 32131.147| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 23720 Z= 0.146 Angle : 0.514 7.633 32384 Z= 0.259 Chirality : 0.037 0.163 3952 Planarity : 0.003 0.033 3988 Dihedral : 3.913 27.783 3312 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.16), residues: 2884 helix: 2.43 (0.11), residues: 2196 sheet: 2.43 (0.62), residues: 68 loop : -1.84 (0.24), residues: 620 =============================================================================== Job complete usr+sys time: 4783.33 seconds wall clock time: 86 minutes 54.11 seconds (5214.11 seconds total)