Starting phenix.real_space_refine on Mon Sep 14 19:10:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11so_76009/09_2026/11so_76009.cif Found real_map, /net/cci-nas-00/data/ceres_data/11so_76009/09_2026/11so_76009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11so_76009/09_2026/11so_76009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11so_76009/09_2026/11so_76009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11so_76009/09_2026/11so_76009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11so_76009/09_2026/11so_76009.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.404 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 19327 2.51 5 N 6069 2.21 5 O 6167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31598 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 4514 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 526} Link IDs: {'PTRANS': 31, 'TRANS': 772} Chain breaks: 2 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1933 Unresolved non-hydrogen angles: 2496 Unresolved non-hydrogen dihedrals: 1593 Unresolved non-hydrogen chiralities: 223 Planarities with less than four sites: {'ASP:plan': 18, 'GLN:plan1': 37, 'PHE:plan': 20, 'ASN:plan1': 17, 'ARG:plan': 44, 'GLU:plan': 31, 'TRP:plan': 15, 'TYR:plan': 13, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 988 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 6.04, per 1000 atoms: 0.19 Number of scatterers: 31598 At special positions: 0 Unit cell: (186.34, 188.881, 167.706, 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 35 16.00 O 6167 8.00 N 6069 7.00 C 19327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10598 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 16 sheets defined 71.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 255 through 306 Processing helix chain 'A' and resid 313 through 326 removed outlier: 4.052A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 362 Proline residue: A 358 - end of helix Processing helix chain 'A' and resid 375 through 426 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 456 through 472 removed outlier: 4.512A pdb=" N SER A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 506 removed outlier: 3.645A pdb=" N LYS A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 530 through 542 Processing helix chain 'A' and resid 549 through 573 Proline residue: A 564 - end of helix Processing helix chain 'A' and resid 589 through 618 removed outlier: 4.146A pdb=" N MET A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Proline residue: A 609 - end of helix removed outlier: 3.575A pdb=" N MET A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 651 Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 672 through 688 removed outlier: 4.125A pdb=" N ILE A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Proline residue: A 679 - end of helix Processing helix chain 'A' and resid 691 through 751 removed outlier: 3.870A pdb=" N GLN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 798 Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 830 through 860 Proline residue: A 852 - end of helix Processing helix chain 'A' and resid 870 through 893 Processing helix chain 'A' and resid 895 through 900 removed outlier: 4.304A pdb=" N LEU A 900 " --> pdb=" O TRP A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 913 " --> pdb=" O VAL A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 932 removed outlier: 3.647A pdb=" N PHE A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 975 Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 4.305A pdb=" N CYS A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU A1055 " --> pdb=" O HIS A1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 306 Processing helix chain 'B' and resid 313 through 326 removed outlier: 4.052A pdb=" N VAL B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 362 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 375 through 426 Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 456 through 472 removed outlier: 4.514A pdb=" N SER B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 506 removed outlier: 3.645A pdb=" N LYS B 506 " --> pdb=" O ARG B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 530 through 542 Processing helix chain 'B' and resid 549 through 573 Proline residue: B 564 - end of helix Processing helix chain 'B' and resid 589 through 618 removed outlier: 4.146A pdb=" N MET B 602 " --> pdb=" O ARG B 598 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 603 " --> pdb=" O TYR B 599 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Proline residue: B 609 - end of helix removed outlier: 3.575A pdb=" N MET B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 651 Processing helix chain 'B' and resid 666 through 672 Processing helix chain 'B' and resid 672 through 688 removed outlier: 4.124A pdb=" N ILE B 676 " --> pdb=" O TRP B 672 " (cutoff:3.500A) Proline residue: B 679 - end of helix Processing helix chain 'B' and resid 691 through 751 removed outlier: 3.870A pdb=" N GLN B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 798 Processing helix chain 'B' and resid 800 through 808 Processing helix chain 'B' and resid 830 through 860 Proline residue: B 852 - end of helix Processing helix chain 'B' and resid 870 through 893 Processing helix chain 'B' and resid 895 through 900 removed outlier: 4.303A pdb=" N LEU B 900 " --> pdb=" O TRP B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE B 913 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 932 removed outlier: 3.647A pdb=" N PHE B 919 " --> pdb=" O LEU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 975 Processing helix chain 'B' and resid 1002 through 1017 removed outlier: 4.306A pdb=" N CYS B1017 " --> pdb=" O ALA B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU B1055 " --> pdb=" O HIS B1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 306 Processing helix chain 'C' and resid 313 through 326 removed outlier: 4.052A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 362 Proline residue: C 358 - end of helix Processing helix chain 'C' and resid 375 through 426 Processing helix chain 'C' and resid 442 through 454 Processing helix chain 'C' and resid 456 through 472 removed outlier: 4.513A pdb=" N SER C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 506 removed outlier: 3.645A pdb=" N LYS C 506 " --> pdb=" O ARG C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 530 Processing helix chain 'C' and resid 530 through 542 Processing helix chain 'C' and resid 549 through 573 Proline residue: C 564 - end of helix Processing helix chain 'C' and resid 589 through 618 removed outlier: 4.146A pdb=" N MET C 602 " --> pdb=" O ARG C 598 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Proline residue: C 609 - end of helix removed outlier: 3.575A pdb=" N MET C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 651 Processing helix chain 'C' and resid 666 through 672 Processing helix chain 'C' and resid 672 through 688 removed outlier: 4.125A pdb=" N ILE C 676 " --> pdb=" O TRP C 672 " (cutoff:3.500A) Proline residue: C 679 - end of helix Processing helix chain 'C' and resid 691 through 751 removed outlier: 3.870A pdb=" N GLN C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 798 Processing helix chain 'C' and resid 800 through 808 Processing helix chain 'C' and resid 830 through 860 Proline residue: C 852 - end of helix Processing helix chain 'C' and resid 870 through 893 Processing helix chain 'C' and resid 895 through 900 removed outlier: 4.304A pdb=" N LEU C 900 " --> pdb=" O TRP C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA C 905 " --> pdb=" O GLN C 901 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE C 913 " --> pdb=" O VAL C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 932 removed outlier: 3.647A pdb=" N PHE C 919 " --> pdb=" O LEU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 975 Processing helix chain 'C' and resid 1002 through 1017 removed outlier: 4.306A pdb=" N CYS C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU C1055 " --> pdb=" O HIS C1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 306 Processing helix chain 'D' and resid 313 through 326 removed outlier: 4.051A pdb=" N VAL D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 362 Proline residue: D 358 - end of helix Processing helix chain 'D' and resid 375 through 426 Processing helix chain 'D' and resid 442 through 454 Processing helix chain 'D' and resid 456 through 472 removed outlier: 4.513A pdb=" N SER D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 506 removed outlier: 3.645A pdb=" N LYS D 506 " --> pdb=" O ARG D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 530 Processing helix chain 'D' and resid 530 through 542 Processing helix chain 'D' and resid 549 through 573 Proline residue: D 564 - end of helix Processing helix chain 'D' and resid 589 through 618 removed outlier: 4.146A pdb=" N MET D 602 " --> pdb=" O ARG D 598 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER D 603 " --> pdb=" O TYR D 599 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Proline residue: D 609 - end of helix removed outlier: 3.575A pdb=" N MET D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 651 Processing helix chain 'D' and resid 666 through 672 Processing helix chain 'D' and resid 672 through 688 removed outlier: 4.125A pdb=" N ILE D 676 " --> pdb=" O TRP D 672 " (cutoff:3.500A) Proline residue: D 679 - end of helix Processing helix chain 'D' and resid 691 through 751 removed outlier: 3.870A pdb=" N GLN D 695 " --> pdb=" O LEU D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 798 Processing helix chain 'D' and resid 800 through 808 Processing helix chain 'D' and resid 830 through 860 Proline residue: D 852 - end of helix Processing helix chain 'D' and resid 870 through 893 Processing helix chain 'D' and resid 895 through 900 removed outlier: 4.303A pdb=" N LEU D 900 " --> pdb=" O TRP D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA D 905 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 907 " --> pdb=" O LEU D 903 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 913 " --> pdb=" O VAL D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 932 removed outlier: 3.647A pdb=" N PHE D 919 " --> pdb=" O LEU D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 975 Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 4.306A pdb=" N CYS D1017 " --> pdb=" O ALA D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU D1055 " --> pdb=" O HIS D1051 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 306 Processing helix chain 'E' and resid 313 through 326 removed outlier: 4.052A pdb=" N VAL E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 362 Proline residue: E 358 - end of helix Processing helix chain 'E' and resid 375 through 426 Processing helix chain 'E' and resid 442 through 454 Processing helix chain 'E' and resid 456 through 472 removed outlier: 4.513A pdb=" N SER E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 472 " --> pdb=" O MET E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 506 removed outlier: 3.645A pdb=" N LYS E 506 " --> pdb=" O ARG E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 530 Processing helix chain 'E' and resid 530 through 542 Processing helix chain 'E' and resid 549 through 573 Proline residue: E 564 - end of helix Processing helix chain 'E' and resid 589 through 618 removed outlier: 4.145A pdb=" N MET E 602 " --> pdb=" O ARG E 598 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER E 603 " --> pdb=" O TYR E 599 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 604 " --> pdb=" O TYR E 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY E 605 " --> pdb=" O LEU E 601 " (cutoff:3.500A) Proline residue: E 609 - end of helix removed outlier: 3.575A pdb=" N MET E 615 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 651 Processing helix chain 'E' and resid 666 through 672 Processing helix chain 'E' and resid 672 through 688 removed outlier: 4.125A pdb=" N ILE E 676 " --> pdb=" O TRP E 672 " (cutoff:3.500A) Proline residue: E 679 - end of helix Processing helix chain 'E' and resid 691 through 751 removed outlier: 3.870A pdb=" N GLN E 695 " --> pdb=" O LEU E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 774 through 798 Processing helix chain 'E' and resid 800 through 808 Processing helix chain 'E' and resid 830 through 860 Proline residue: E 852 - end of helix Processing helix chain 'E' and resid 870 through 893 Processing helix chain 'E' and resid 895 through 900 removed outlier: 4.304A pdb=" N LEU E 900 " --> pdb=" O TRP E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA E 905 " --> pdb=" O GLN E 901 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU E 907 " --> pdb=" O LEU E 903 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE E 913 " --> pdb=" O VAL E 909 " (cutoff:3.500A) Processing helix chain 'E' and resid 915 through 932 removed outlier: 3.648A pdb=" N PHE E 919 " --> pdb=" O LEU E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 975 Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 4.307A pdb=" N CYS E1017 " --> pdb=" O ALA E1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU E1055 " --> pdb=" O HIS E1051 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 306 Processing helix chain 'F' and resid 313 through 326 removed outlier: 4.052A pdb=" N VAL F 324 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 362 Proline residue: F 358 - end of helix Processing helix chain 'F' and resid 375 through 426 Processing helix chain 'F' and resid 442 through 454 Processing helix chain 'F' and resid 456 through 472 removed outlier: 4.513A pdb=" N SER F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER F 472 " --> pdb=" O MET F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 506 removed outlier: 3.645A pdb=" N LYS F 506 " --> pdb=" O ARG F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 530 Processing helix chain 'F' and resid 530 through 542 Processing helix chain 'F' and resid 549 through 573 Proline residue: F 564 - end of helix Processing helix chain 'F' and resid 589 through 618 removed outlier: 4.146A pdb=" N MET F 602 " --> pdb=" O ARG F 598 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER F 603 " --> pdb=" O TYR F 599 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE F 604 " --> pdb=" O TYR F 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY F 605 " --> pdb=" O LEU F 601 " (cutoff:3.500A) Proline residue: F 609 - end of helix removed outlier: 3.576A pdb=" N MET F 615 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 624 through 651 Processing helix chain 'F' and resid 666 through 672 Processing helix chain 'F' and resid 672 through 688 removed outlier: 4.125A pdb=" N ILE F 676 " --> pdb=" O TRP F 672 " (cutoff:3.500A) Proline residue: F 679 - end of helix Processing helix chain 'F' and resid 691 through 751 removed outlier: 3.870A pdb=" N GLN F 695 " --> pdb=" O LEU F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 774 through 798 Processing helix chain 'F' and resid 800 through 808 Processing helix chain 'F' and resid 830 through 860 Proline residue: F 852 - end of helix Processing helix chain 'F' and resid 870 through 893 Processing helix chain 'F' and resid 895 through 900 removed outlier: 4.304A pdb=" N LEU F 900 " --> pdb=" O TRP F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA F 905 " --> pdb=" O GLN F 901 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 907 " --> pdb=" O LEU F 903 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE F 913 " --> pdb=" O VAL F 909 " (cutoff:3.500A) Processing helix chain 'F' and resid 915 through 932 removed outlier: 3.647A pdb=" N PHE F 919 " --> pdb=" O LEU F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 972 through 975 Processing helix chain 'F' and resid 1002 through 1017 removed outlier: 4.306A pdb=" N CYS F1017 " --> pdb=" O ALA F1013 " (cutoff:3.500A) Processing helix chain 'F' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU F1055 " --> pdb=" O HIS F1051 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 306 Processing helix chain 'G' and resid 313 through 326 removed outlier: 4.051A pdb=" N VAL G 324 " --> pdb=" O LEU G 320 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 362 Proline residue: G 358 - end of helix Processing helix chain 'G' and resid 375 through 426 Processing helix chain 'G' and resid 442 through 454 Processing helix chain 'G' and resid 456 through 472 removed outlier: 4.513A pdb=" N SER G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER G 472 " --> pdb=" O MET G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 506 removed outlier: 3.644A pdb=" N LYS G 506 " --> pdb=" O ARG G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 530 Processing helix chain 'G' and resid 530 through 542 Processing helix chain 'G' and resid 549 through 573 Proline residue: G 564 - end of helix Processing helix chain 'G' and resid 589 through 618 removed outlier: 4.146A pdb=" N MET G 602 " --> pdb=" O ARG G 598 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER G 603 " --> pdb=" O TYR G 599 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE G 604 " --> pdb=" O TYR G 600 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY G 605 " --> pdb=" O LEU G 601 " (cutoff:3.500A) Proline residue: G 609 - end of helix removed outlier: 3.576A pdb=" N MET G 615 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP G 618 " --> pdb=" O LEU G 614 " (cutoff:3.500A) Processing helix chain 'G' and resid 624 through 651 Processing helix chain 'G' and resid 666 through 672 Processing helix chain 'G' and resid 672 through 688 removed outlier: 4.125A pdb=" N ILE G 676 " --> pdb=" O TRP G 672 " (cutoff:3.500A) Proline residue: G 679 - end of helix Processing helix chain 'G' and resid 691 through 751 removed outlier: 3.869A pdb=" N GLN G 695 " --> pdb=" O LEU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 798 Processing helix chain 'G' and resid 800 through 808 Processing helix chain 'G' and resid 830 through 860 Proline residue: G 852 - end of helix Processing helix chain 'G' and resid 870 through 893 Processing helix chain 'G' and resid 895 through 900 removed outlier: 4.304A pdb=" N LEU G 900 " --> pdb=" O TRP G 897 " (cutoff:3.500A) Processing helix chain 'G' and resid 901 through 913 removed outlier: 4.353A pdb=" N ALA G 905 " --> pdb=" O GLN G 901 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU G 907 " --> pdb=" O LEU G 903 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE G 913 " --> pdb=" O VAL G 909 " (cutoff:3.500A) Processing helix chain 'G' and resid 915 through 932 removed outlier: 3.647A pdb=" N PHE G 919 " --> pdb=" O LEU G 915 " (cutoff:3.500A) Processing helix chain 'G' and resid 972 through 975 Processing helix chain 'G' and resid 1002 through 1017 removed outlier: 4.306A pdb=" N CYS G1017 " --> pdb=" O ALA G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1051 through 1071 removed outlier: 3.667A pdb=" N LEU G1055 " --> pdb=" O HIS G1051 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 814 through 820 removed outlier: 3.864A pdb=" N TRP A 814 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 939 through 942 removed outlier: 6.886A pdb=" N THR A 958 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE A 952 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 956 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU A 966 " --> pdb=" O ASN B 981 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 981 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 979 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 958 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 952 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 956 " --> pdb=" O ILE B 952 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLU B 966 " --> pdb=" O ASN C 981 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 981 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 979 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR C 958 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE C 952 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 956 " --> pdb=" O ILE C 952 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU C 966 " --> pdb=" O ASN D 981 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 981 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 958 " --> pdb=" O THR D 950 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE D 952 " --> pdb=" O ALA D 956 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA D 956 " --> pdb=" O ILE D 952 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU D 966 " --> pdb=" O ASN E 981 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN E 981 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR E 958 " --> pdb=" O THR E 950 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE E 952 " --> pdb=" O ALA E 956 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA E 956 " --> pdb=" O ILE E 952 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLU E 966 " --> pdb=" O ASN F 981 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN F 981 " --> pdb=" O GLU E 966 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE F 979 " --> pdb=" O ILE E 968 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR F 958 " --> pdb=" O THR F 950 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE F 952 " --> pdb=" O ALA F 956 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA F 956 " --> pdb=" O ILE F 952 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU F 966 " --> pdb=" O ASN G 981 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN G 981 " --> pdb=" O GLU F 966 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR G 958 " --> pdb=" O THR G 950 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE G 952 " --> pdb=" O ALA G 956 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA G 956 " --> pdb=" O ILE G 952 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU G 966 " --> pdb=" O ASN A 981 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 981 " --> pdb=" O GLU G 966 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 979 " --> pdb=" O ILE G 968 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 990 through 997 removed outlier: 7.096A pdb=" N ILE A1039 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A1027 " --> pdb=" O ARG A1043 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1078 through 1083 removed outlier: 3.610A pdb=" N ARG B1082 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1081 " --> pdb=" O ARG B1082 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C1082 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B1081 " --> pdb=" O ARG C1082 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D1082 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C1081 " --> pdb=" O ARG D1082 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E1082 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D1081 " --> pdb=" O ARG E1082 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG F1082 " --> pdb=" O PHE E1079 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET E1081 " --> pdb=" O ARG F1082 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG G1082 " --> pdb=" O PHE F1079 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET F1081 " --> pdb=" O ARG G1082 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N PHE G1079 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN A1080 " --> pdb=" O PHE G1079 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET G1081 " --> pdb=" O GLN A1080 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG A1082 " --> pdb=" O MET G1081 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU G1083 " --> pdb=" O ARG A1082 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 814 through 820 removed outlier: 3.864A pdb=" N TRP B 814 " --> pdb=" O ILE B 829 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 990 through 997 removed outlier: 7.097A pdb=" N ILE B1039 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B1027 " --> pdb=" O ARG B1043 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 814 through 820 removed outlier: 3.864A pdb=" N TRP C 814 " --> pdb=" O ILE C 829 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 990 through 997 removed outlier: 7.096A pdb=" N ILE C1039 " --> pdb=" O VAL C1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C1027 " --> pdb=" O ARG C1043 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 814 through 820 removed outlier: 3.864A pdb=" N TRP D 814 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 990 through 997 removed outlier: 7.096A pdb=" N ILE D1039 " --> pdb=" O VAL D1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D1027 " --> pdb=" O ARG D1043 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 814 through 820 removed outlier: 3.865A pdb=" N TRP E 814 " --> pdb=" O ILE E 829 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 990 through 997 removed outlier: 7.096A pdb=" N ILE E1039 " --> pdb=" O VAL E1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E1027 " --> pdb=" O ARG E1043 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 814 through 820 removed outlier: 3.865A pdb=" N TRP F 814 " --> pdb=" O ILE F 829 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 990 through 997 removed outlier: 7.097A pdb=" N ILE F1039 " --> pdb=" O VAL F1031 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F1027 " --> pdb=" O ARG F1043 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 814 through 820 removed outlier: 3.864A pdb=" N TRP G 814 " --> pdb=" O ILE G 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 990 through 997 removed outlier: 7.096A pdb=" N ILE G1039 " --> pdb=" O VAL G1031 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G1027 " --> pdb=" O ARG G1043 " (cutoff:3.500A) 3299 hydrogen bonds defined for protein. 9762 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: 7.40 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6189 1.31 - 1.44: 7038 1.44 - 1.56: 18504 1.56 - 1.69: 14 1.69 - 1.81: 63 Bond restraints: 31808 Sorted by residual: bond pdb=" CA LEU C 711 " pdb=" C LEU C 711 " ideal model delta sigma weight residual 1.523 1.435 0.087 1.37e-02 5.33e+03 4.08e+01 bond pdb=" CA LEU F 711 " pdb=" C LEU F 711 " ideal model delta sigma weight residual 1.523 1.435 0.087 1.37e-02 5.33e+03 4.08e+01 bond pdb=" CA LEU B 711 " pdb=" C LEU B 711 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.37e-02 5.33e+03 4.06e+01 bond pdb=" CA LEU E 711 " pdb=" C LEU E 711 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.37e-02 5.33e+03 4.04e+01 bond pdb=" CA LEU A 711 " pdb=" C LEU A 711 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.37e-02 5.33e+03 4.02e+01 ... (remaining 31803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 43124 3.89 - 7.78: 693 7.78 - 11.66: 52 11.66 - 15.55: 35 15.55 - 19.44: 49 Bond angle restraints: 43953 Sorted by residual: angle pdb=" N ASP D 963 " pdb=" CA ASP D 963 " pdb=" C ASP D 963 " ideal model delta sigma weight residual 112.92 96.55 16.37 1.23e+00 6.61e-01 1.77e+02 angle pdb=" N ASP C 963 " pdb=" CA ASP C 963 " pdb=" C ASP C 963 " ideal model delta sigma weight residual 112.92 96.56 16.36 1.23e+00 6.61e-01 1.77e+02 angle pdb=" N ASP B 963 " pdb=" CA ASP B 963 " pdb=" C ASP B 963 " ideal model delta sigma weight residual 112.92 96.58 16.34 1.23e+00 6.61e-01 1.77e+02 angle pdb=" N ASP E 963 " pdb=" CA ASP E 963 " pdb=" C ASP E 963 " ideal model delta sigma weight residual 112.92 96.58 16.34 1.23e+00 6.61e-01 1.76e+02 angle pdb=" N ASP A 963 " pdb=" CA ASP A 963 " pdb=" C ASP A 963 " ideal model delta sigma weight residual 112.92 96.59 16.33 1.23e+00 6.61e-01 1.76e+02 ... (remaining 43948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.70: 17185 12.70 - 25.40: 1022 25.40 - 38.10: 301 38.10 - 50.79: 147 50.79 - 63.49: 49 Dihedral angle restraints: 18704 sinusoidal: 2492 harmonic: 16212 Sorted by residual: dihedral pdb=" CA ALA B 573 " pdb=" C ALA B 573 " pdb=" N THR B 574 " pdb=" CA THR B 574 " ideal model delta harmonic sigma weight residual 180.00 140.61 39.39 0 5.00e+00 4.00e-02 6.21e+01 dihedral pdb=" CA ALA D 573 " pdb=" C ALA D 573 " pdb=" N THR D 574 " pdb=" CA THR D 574 " ideal model delta harmonic sigma weight residual 180.00 140.61 39.39 0 5.00e+00 4.00e-02 6.21e+01 dihedral pdb=" CA ALA C 573 " pdb=" C ALA C 573 " pdb=" N THR C 574 " pdb=" CA THR C 574 " ideal model delta harmonic sigma weight residual 180.00 140.62 39.38 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 18701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 5677 0.162 - 0.324: 56 0.324 - 0.485: 7 0.485 - 0.647: 7 0.647 - 0.809: 7 Chirality restraints: 5754 Sorted by residual: chirality pdb=" CA MET D1053 " pdb=" N MET D1053 " pdb=" C MET D1053 " pdb=" CB MET D1053 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA MET G1053 " pdb=" N MET G1053 " pdb=" C MET G1053 " pdb=" CB MET G1053 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" CA MET C1053 " pdb=" N MET C1053 " pdb=" C MET C1053 " pdb=" CB MET C1053 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 5751 not shown) Planarity restraints: 6132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D1072 " -0.056 2.00e-02 2.50e+03 1.13e-01 1.27e+02 pdb=" C ILE D1072 " 0.195 2.00e-02 2.50e+03 pdb=" O ILE D1072 " -0.075 2.00e-02 2.50e+03 pdb=" N ASP D1073 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F1072 " -0.056 2.00e-02 2.50e+03 1.13e-01 1.27e+02 pdb=" C ILE F1072 " 0.195 2.00e-02 2.50e+03 pdb=" O ILE F1072 " -0.075 2.00e-02 2.50e+03 pdb=" N ASP F1073 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1072 " -0.056 2.00e-02 2.50e+03 1.13e-01 1.27e+02 pdb=" C ILE C1072 " 0.195 2.00e-02 2.50e+03 pdb=" O ILE C1072 " -0.075 2.00e-02 2.50e+03 pdb=" N ASP C1073 " -0.064 2.00e-02 2.50e+03 ... (remaining 6129 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 456 2.57 - 3.15: 28573 3.15 - 3.74: 54175 3.74 - 4.32: 59692 4.32 - 4.90: 93637 Nonbonded interactions: 236533 Sorted by model distance: nonbonded pdb=" OE2 GLU A1084 " pdb=" NE2 GLN G1080 " model vdw 1.989 3.120 nonbonded pdb=" NE2 GLN F1080 " pdb=" OE2 GLU G1084 " model vdw 1.998 3.120 nonbonded pdb=" NE2 GLN C1080 " pdb=" OE2 GLU D1084 " model vdw 2.018 3.120 nonbonded pdb=" NE2 GLN D1080 " pdb=" OE2 GLU E1084 " model vdw 2.029 3.120 nonbonded pdb=" NE2 GLN A1080 " pdb=" OE2 GLU B1084 " model vdw 2.033 3.120 ... (remaining 236528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.160 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 : 0.009 0.087 31808 Z= 0.656 Angle : 1.252 19.440 43953 Z= 0.804 Chirality : 0.061 0.809 5754 Planarity : 0.010 0.191 6132 Dihedral : 12.281 63.492 8106 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 1.63 % Allowed : 1.38 % Favored : 96.99 % Rotamer: Outliers : 0.63 % Allowed : 33.91 % Favored : 65.46 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 5586 helix: 1.60 (0.09), residues: 3535 sheet: 0.57 (0.28), residues: 322 loop : -2.08 (0.16), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 964 TYR 0.004 0.000 TYR B1045 PHE 0.013 0.002 PHE D 913 TRP 0.007 0.001 TRP C 962 HIS 0.002 0.001 HIS G1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00883 / 0.66 (31808) covalent geometry : angle 1.25210 / 0.80 (43953) hydrogen bonds : bond 0.13332 / 10.04 ( 3299) hydrogen bonds : angle 6.86422 / 5.22 ( 9762) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 540 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1022 ASP cc_start: 0.7800 (m-30) cc_final: 0.7586 (m-30) REVERT: B 1049 MET cc_start: 0.0950 (tmm) cc_final: -0.0291 (mtm) REVERT: F 1022 ASP cc_start: 0.7972 (m-30) cc_final: 0.7724 (m-30) outliers start: 7 outliers final: 7 residues processed: 545 average time/residue: 0.2051 time to fit residues: 175.1642 Evaluate side-chains 370 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 363 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 0.0970 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1051 HIS ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 HIS ** B1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 HIS ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 HIS ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1057 HIS ** D1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1068 HIS F 978 GLN ** F1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1068 HIS G1051 HIS G1057 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.084506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059868 restraints weight = 270260.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060565 restraints weight = 219819.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061269 restraints weight = 191504.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.061531 restraints weight = 174880.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061809 restraints weight = 165118.030| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 31808 Z= 0.274 Angle : 0.793 21.150 43953 Z= 0.434 Chirality : 0.044 0.356 5754 Planarity : 0.008 0.186 6132 Dihedral : 6.215 29.536 5691 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 1.25 % Allowed : 7.61 % Favored : 91.14 % Rotamer: Outliers : 0.81 % Allowed : 6.06 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 5586 helix: 1.47 (0.08), residues: 3675 sheet: 1.31 (0.29), residues: 301 loop : -1.91 (0.18), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG F 964 TYR 0.015 0.001 TYR D1045 PHE 0.023 0.002 PHE D1079 TRP 0.035 0.002 TRP C 902 HIS 0.009 0.002 HIS C1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.27 (31808) covalent geometry : angle 0.79305 / 0.43 (43953) hydrogen bonds : bond 0.06620 / 5.00 ( 3299) hydrogen bonds : angle 5.57862 / 4.27 ( 9762) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 384 time to evaluate : 1.147 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: A 931 GLU cc_start: 0.7539 (tt0) cc_final: 0.7311 (tt0) REVERT: A 945 LEU cc_start: 0.8983 (mm) cc_final: 0.8607 (mp) REVERT: B 931 GLU cc_start: 0.7623 (tt0) cc_final: 0.7408 (tt0) REVERT: B 944 ASP cc_start: 0.7821 (p0) cc_final: 0.7602 (p0) REVERT: B 1053 MET cc_start: 0.8830 (mtm) cc_final: 0.8593 (mmm) REVERT: C 945 LEU cc_start: 0.8970 (mm) cc_final: 0.8697 (mp) REVERT: C 965 LYS cc_start: 0.7426 (mmtm) cc_final: 0.7078 (mmtp) REVERT: D 945 LEU cc_start: 0.8909 (mm) cc_final: 0.8652 (mp) REVERT: D 965 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7745 (mmtp) REVERT: D 994 THR cc_start: 0.8320 (m) cc_final: 0.7570 (m) REVERT: E 931 GLU cc_start: 0.7557 (tt0) cc_final: 0.7169 (tt0) REVERT: E 945 LEU cc_start: 0.9079 (mm) cc_final: 0.8836 (mp) REVERT: F 931 GLU cc_start: 0.7647 (tt0) cc_final: 0.7193 (tt0) REVERT: F 945 LEU cc_start: 0.9094 (mm) cc_final: 0.8866 (mp) REVERT: G 945 LEU cc_start: 0.8979 (mm) cc_final: 0.8721 (mp) REVERT: G 1035 GLN cc_start: 0.9020 (mp10) cc_final: 0.8753 (mp10) outliers start: 9 outliers final: 4 residues processed: 386 average time/residue: 0.1443 time to fit residues: 99.9568 Evaluate side-chains 326 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 322 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 236 optimal weight: 0.9990 chunk 233 optimal weight: 0.4980 chunk 406 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 312 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 434 optimal weight: 0.0270 chunk 405 optimal weight: 20.0000 chunk 359 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1051 HIS A1057 HIS B 978 GLN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 HIS B1060 HIS B1068 HIS ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS C1068 HIS ** D 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 HIS D1060 HIS D1068 HIS E 978 GLN E1051 HIS E1060 HIS E1068 HIS E1080 GLN F1051 HIS F1057 HIS F1060 HIS F1068 HIS G 978 GLN G1051 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.086255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.061553 restraints weight = 245825.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061868 restraints weight = 206215.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062265 restraints weight = 180868.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062553 restraints weight = 167824.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.062690 restraints weight = 159561.744| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31808 Z= 0.153 Angle : 0.643 18.277 43953 Z= 0.347 Chirality : 0.042 0.272 5754 Planarity : 0.006 0.167 6132 Dihedral : 5.875 28.944 5691 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 1.25 % Allowed : 5.67 % Favored : 93.07 % Rotamer: Outliers : 0.27 % Allowed : 5.88 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.12), residues: 5586 helix: 1.88 (0.08), residues: 3780 sheet: 1.24 (0.28), residues: 322 loop : -2.01 (0.18), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 964 TYR 0.006 0.000 TYR E1045 PHE 0.032 0.001 PHE F1076 TRP 0.041 0.002 TRP E 902 HIS 0.010 0.002 HIS G1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (31808) covalent geometry : angle 0.64253 / 0.35 (43953) hydrogen bonds : bond 0.05306 / 4.02 ( 3299) hydrogen bonds : angle 5.22525 / 3.99 ( 9762) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 383 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 LEU cc_start: 0.8790 (mm) cc_final: 0.8451 (mp) REVERT: A 1004 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 945 LEU cc_start: 0.8922 (mm) cc_final: 0.8620 (mp) REVERT: C 945 LEU cc_start: 0.8862 (mm) cc_final: 0.8581 (mp) REVERT: C 965 LYS cc_start: 0.7318 (mmtm) cc_final: 0.7020 (mmtp) REVERT: D 945 LEU cc_start: 0.8868 (mm) cc_final: 0.8564 (mp) REVERT: E 931 GLU cc_start: 0.7523 (tt0) cc_final: 0.7143 (tt0) REVERT: E 945 LEU cc_start: 0.8952 (mm) cc_final: 0.8737 (mp) REVERT: E 965 LYS cc_start: 0.7498 (mmtp) cc_final: 0.7277 (mmtp) REVERT: E 1016 ARG cc_start: 0.7317 (tmm160) cc_final: 0.7117 (ttp80) REVERT: F 931 GLU cc_start: 0.7416 (tt0) cc_final: 0.7082 (tt0) REVERT: F 945 LEU cc_start: 0.9001 (mm) cc_final: 0.8759 (mp) REVERT: F 1032 ASP cc_start: 0.6913 (t0) cc_final: 0.6688 (t0) REVERT: F 1034 GLN cc_start: 0.8320 (mp-120) cc_final: 0.7913 (tp40) REVERT: G 931 GLU cc_start: 0.7374 (tt0) cc_final: 0.7141 (tt0) REVERT: G 945 LEU cc_start: 0.8806 (mm) cc_final: 0.8543 (mp) REVERT: G 1022 ASP cc_start: 0.8258 (t70) cc_final: 0.8034 (t0) outliers start: 3 outliers final: 0 residues processed: 383 average time/residue: 0.1595 time to fit residues: 105.2290 Evaluate side-chains 320 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 110 optimal weight: 9.9990 chunk 335 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 232 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 chunk 310 optimal weight: 3.9990 chunk 504 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1034 GLN A1051 HIS B 978 GLN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 HIS B1060 HIS B1068 HIS ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1068 HIS D1051 HIS ** D1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1068 HIS ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1051 HIS ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1068 HIS ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1034 GLN F1051 HIS ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 978 GLN G1051 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.083463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059221 restraints weight = 265741.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059927 restraints weight = 221184.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060267 restraints weight = 192537.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.060408 restraints weight = 176184.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060868 restraints weight = 168026.996| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 31808 Z= 0.194 Angle : 0.675 20.760 43953 Z= 0.365 Chirality : 0.043 0.302 5754 Planarity : 0.006 0.167 6132 Dihedral : 5.760 28.331 5691 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 1.25 % Allowed : 7.95 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.12), residues: 5586 helix: 2.02 (0.08), residues: 3780 sheet: 1.23 (0.29), residues: 322 loop : -1.95 (0.18), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 964 TYR 0.013 0.001 TYR E1045 PHE 0.018 0.001 PHE B 974 TRP 0.036 0.002 TRP A 902 HIS 0.014 0.002 HIS D1060 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (31808) covalent geometry : angle 0.67501 / 0.36 (43953) hydrogen bonds : bond 0.05503 / 4.17 ( 3299) hydrogen bonds : angle 5.12245 / 3.93 ( 9762) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 931 GLU cc_start: 0.7754 (tt0) cc_final: 0.7397 (tt0) REVERT: A 945 LEU cc_start: 0.9099 (mm) cc_final: 0.8808 (mp) REVERT: A 1034 GLN cc_start: 0.8277 (mp10) cc_final: 0.7728 (tp40) REVERT: C 931 GLU cc_start: 0.7596 (tt0) cc_final: 0.7369 (tt0) REVERT: C 965 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8304 (mmtp) REVERT: D 931 GLU cc_start: 0.7601 (tt0) cc_final: 0.7364 (tt0) REVERT: D 945 LEU cc_start: 0.9074 (mm) cc_final: 0.8782 (mp) REVERT: E 931 GLU cc_start: 0.7597 (tt0) cc_final: 0.7106 (tt0) REVERT: E 944 ASP cc_start: 0.7903 (p0) cc_final: 0.7698 (p0) REVERT: E 945 LEU cc_start: 0.9125 (mm) cc_final: 0.8918 (mp) REVERT: E 965 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8076 (mmtp) REVERT: E 982 TRP cc_start: 0.7067 (m100) cc_final: 0.6749 (m100) REVERT: E 1016 ARG cc_start: 0.7559 (tmm160) cc_final: 0.7131 (ttp80) REVERT: F 945 LEU cc_start: 0.9196 (mm) cc_final: 0.8905 (mp) REVERT: F 965 LYS cc_start: 0.8570 (mmtp) cc_final: 0.8074 (mmtp) REVERT: F 994 THR cc_start: 0.8213 (m) cc_final: 0.7885 (m) REVERT: F 1032 ASP cc_start: 0.7341 (t0) cc_final: 0.7099 (t0) REVERT: F 1034 GLN cc_start: 0.8274 (mp10) cc_final: 0.7982 (tp40) REVERT: G 931 GLU cc_start: 0.7536 (tt0) cc_final: 0.7120 (tt0) REVERT: G 965 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7903 (mmtp) REVERT: G 994 THR cc_start: 0.8140 (m) cc_final: 0.7803 (p) REVERT: G 1022 ASP cc_start: 0.8360 (t70) cc_final: 0.8131 (t0) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1471 time to fit residues: 95.6505 Evaluate side-chains 323 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 458 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 19 optimal weight: 50.0000 chunk 470 optimal weight: 0.0060 chunk 277 optimal weight: 10.0000 chunk 173 optimal weight: 50.0000 chunk 290 optimal weight: 20.0000 chunk 513 optimal weight: 6.9990 chunk 523 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1038 GLN A1051 HIS ** B1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1068 HIS ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1068 HIS D1034 GLN D1051 HIS ** D1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1068 HIS E 978 GLN E1051 HIS ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1068 HIS ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1051 HIS ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1068 HIS ** G 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1051 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.081091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056351 restraints weight = 264399.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056983 restraints weight = 218377.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.057243 restraints weight = 188316.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057881 restraints weight = 175167.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058082 restraints weight = 163585.550| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 31808 Z= 0.230 Angle : 0.670 14.804 43953 Z= 0.383 Chirality : 0.043 0.226 5754 Planarity : 0.005 0.119 6132 Dihedral : 5.949 29.459 5691 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.55 % Favored : 91.42 % Rotamer: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.12), residues: 5586 helix: 2.06 (0.08), residues: 3822 sheet: 0.99 (0.30), residues: 336 loop : -2.12 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1082 TYR 0.010 0.001 TYR D1045 PHE 0.031 0.002 PHE F 922 TRP 0.036 0.003 TRP E 902 HIS 0.016 0.003 HIS B1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.23 (31808) covalent geometry : angle 0.67016 / 0.38 (43953) hydrogen bonds : bond 0.05808 / 4.40 ( 3299) hydrogen bonds : angle 5.12943 / 3.93 ( 9762) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 931 GLU cc_start: 0.7668 (tt0) cc_final: 0.7403 (tt0) REVERT: A 965 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8739 (mmtp) REVERT: B 917 GLU cc_start: 0.7697 (mp0) cc_final: 0.7162 (mp0) REVERT: B 965 LYS cc_start: 0.8714 (mmpt) cc_final: 0.8396 (mmmt) REVERT: C 927 ILE cc_start: 0.8876 (pt) cc_final: 0.8176 (tp) REVERT: D 926 LEU cc_start: 0.8590 (mm) cc_final: 0.7322 (mm) REVERT: D 927 ILE cc_start: 0.9072 (tp) cc_final: 0.8630 (tp) REVERT: E 931 GLU cc_start: 0.7611 (tt0) cc_final: 0.7249 (tt0) REVERT: E 965 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8496 (mmtp) REVERT: E 994 THR cc_start: 0.8359 (m) cc_final: 0.8012 (m) REVERT: E 1016 ARG cc_start: 0.7943 (tmm160) cc_final: 0.7740 (ttp80) REVERT: F 944 ASP cc_start: 0.8004 (p0) cc_final: 0.7526 (t0) REVERT: F 945 LEU cc_start: 0.9163 (mm) cc_final: 0.8939 (mp) REVERT: G 931 GLU cc_start: 0.7570 (tt0) cc_final: 0.7320 (tt0) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1617 time to fit residues: 110.7870 Evaluate side-chains 335 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 465 optimal weight: 5.9990 chunk 333 optimal weight: 50.0000 chunk 412 optimal weight: 50.0000 chunk 81 optimal weight: 40.0000 chunk 390 optimal weight: 0.5980 chunk 197 optimal weight: 8.9990 chunk 169 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 99 optimal weight: 0.0570 overall best weight: 4.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1051 HIS B1051 HIS ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1051 HIS ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 978 GLN F1051 HIS ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.078405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052962 restraints weight = 259696.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053622 restraints weight = 211922.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.054217 restraints weight = 186584.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054455 restraints weight = 172126.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054714 restraints weight = 162595.305| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 31808 Z= 0.315 Angle : 0.757 12.664 43953 Z= 0.435 Chirality : 0.044 0.191 5754 Planarity : 0.005 0.083 6132 Dihedral : 6.251 31.297 5691 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.12), residues: 5586 helix: 2.01 (0.08), residues: 3794 sheet: 0.66 (0.30), residues: 322 loop : -2.25 (0.18), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1082 TYR 0.011 0.001 TYR F1045 PHE 0.048 0.003 PHE F1029 TRP 0.031 0.002 TRP D 982 HIS 0.015 0.004 HIS B1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.31 (31808) covalent geometry : angle 0.75689 / 0.43 (43953) hydrogen bonds : bond 0.06672 / 5.05 ( 3299) hydrogen bonds : angle 5.43400 / 4.16 ( 9762) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.193 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: A 919 PHE cc_start: 0.8641 (t80) cc_final: 0.8288 (t80) REVERT: A 1008 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7872 (tm-30) REVERT: B 911 LEU cc_start: 0.8787 (tp) cc_final: 0.8535 (tp) REVERT: B 919 PHE cc_start: 0.8480 (t80) cc_final: 0.8151 (t80) REVERT: C 931 GLU cc_start: 0.8638 (mp0) cc_final: 0.8207 (mp0) REVERT: C 944 ASP cc_start: 0.8187 (p0) cc_final: 0.7772 (t70) REVERT: D 919 PHE cc_start: 0.8637 (t80) cc_final: 0.8299 (t80) REVERT: D 926 LEU cc_start: 0.8633 (mm) cc_final: 0.8031 (mm) REVERT: D 927 ILE cc_start: 0.9274 (tp) cc_final: 0.8790 (tp) REVERT: D 945 LEU cc_start: 0.9140 (mt) cc_final: 0.8800 (pp) REVERT: E 919 PHE cc_start: 0.8674 (t80) cc_final: 0.8453 (t80) REVERT: E 965 LYS cc_start: 0.9140 (mmtp) cc_final: 0.8723 (mmtp) REVERT: E 1016 ARG cc_start: 0.8283 (tmm160) cc_final: 0.7547 (ttp80) REVERT: F 944 ASP cc_start: 0.8110 (p0) cc_final: 0.7771 (t70) REVERT: F 1008 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7717 (tm-30) REVERT: F 1034 GLN cc_start: 0.8708 (tp40) cc_final: 0.8417 (tp40) REVERT: G 931 GLU cc_start: 0.7663 (tt0) cc_final: 0.7300 (tt0) REVERT: G 965 LYS cc_start: 0.9141 (mmtp) cc_final: 0.8932 (mmtp) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1553 time to fit residues: 106.4466 Evaluate side-chains 329 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 323 optimal weight: 20.0000 chunk 431 optimal weight: 0.0370 chunk 261 optimal weight: 10.0000 chunk 153 optimal weight: 0.0020 chunk 250 optimal weight: 0.6980 chunk 9 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 545 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 376 optimal weight: 0.7980 chunk 265 optimal weight: 20.0000 overall best weight: 0.9068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 GLN ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 GLN ** D1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1068 HIS ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.080968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055774 restraints weight = 259471.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056402 restraints weight = 211157.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057061 restraints weight = 186256.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057062 restraints weight = 169376.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.057201 restraints weight = 169360.771| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31808 Z= 0.156 Angle : 0.615 14.531 43953 Z= 0.345 Chirality : 0.042 0.181 5754 Planarity : 0.004 0.045 6132 Dihedral : 5.920 29.970 5691 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.78 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.12), residues: 5586 helix: 2.11 (0.08), residues: 3878 sheet: 1.07 (0.30), residues: 322 loop : -2.40 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 990 TYR 0.008 0.001 TYR C1045 PHE 0.027 0.002 PHE G1029 TRP 0.016 0.002 TRP D 982 HIS 0.021 0.004 HIS C1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (31808) covalent geometry : angle 0.61509 / 0.35 (43953) hydrogen bonds : bond 0.05140 / 3.90 ( 3299) hydrogen bonds : angle 4.96987 / 3.80 ( 9762) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 919 PHE cc_start: 0.8502 (t80) cc_final: 0.8274 (t80) REVERT: A 1016 ARG cc_start: 0.8708 (mmp80) cc_final: 0.8392 (mtt180) REVERT: B 919 PHE cc_start: 0.8385 (t80) cc_final: 0.8003 (t80) REVERT: B 927 ILE cc_start: 0.9130 (tp) cc_final: 0.8930 (tp) REVERT: B 965 LYS cc_start: 0.8832 (mmpt) cc_final: 0.8578 (mmmt) REVERT: B 1016 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8455 (tmm160) REVERT: B 1034 GLN cc_start: 0.8051 (tp40) cc_final: 0.7763 (tp40) REVERT: C 927 ILE cc_start: 0.9045 (tp) cc_final: 0.8566 (tp) REVERT: C 931 GLU cc_start: 0.8180 (mp0) cc_final: 0.7735 (mp0) REVERT: C 1034 GLN cc_start: 0.8037 (tp40) cc_final: 0.7682 (tp40) REVERT: D 919 PHE cc_start: 0.8473 (t80) cc_final: 0.7869 (t80) REVERT: D 923 ILE cc_start: 0.8989 (tp) cc_final: 0.8782 (tp) REVERT: D 926 LEU cc_start: 0.8957 (mm) cc_final: 0.8031 (mt) REVERT: D 927 ILE cc_start: 0.9238 (tp) cc_final: 0.8845 (tp) REVERT: D 930 PHE cc_start: 0.7470 (m-80) cc_final: 0.7131 (m-80) REVERT: D 945 LEU cc_start: 0.9097 (mt) cc_final: 0.8755 (pp) REVERT: D 1022 ASP cc_start: 0.8351 (m-30) cc_final: 0.8137 (m-30) REVERT: E 916 GLN cc_start: 0.8778 (pm20) cc_final: 0.8471 (pm20) REVERT: E 919 PHE cc_start: 0.8540 (t80) cc_final: 0.8276 (t80) REVERT: E 944 ASP cc_start: 0.7981 (p0) cc_final: 0.7714 (p0) REVERT: E 994 THR cc_start: 0.7965 (p) cc_final: 0.7197 (p) REVERT: E 1016 ARG cc_start: 0.8322 (tmm160) cc_final: 0.7579 (ttp80) REVERT: E 1034 GLN cc_start: 0.7516 (tp40) cc_final: 0.7256 (tp40) REVERT: F 1034 GLN cc_start: 0.8420 (tp40) cc_final: 0.7976 (tp40) REVERT: G 931 GLU cc_start: 0.7479 (tt0) cc_final: 0.7222 (tt0) REVERT: G 1016 ARG cc_start: 0.8784 (mmp80) cc_final: 0.8244 (ttp80) REVERT: G 1022 ASP cc_start: 0.8371 (t70) cc_final: 0.8159 (t0) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1711 time to fit residues: 116.8115 Evaluate side-chains 342 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 375 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 495 optimal weight: 20.0000 chunk 401 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 530 optimal weight: 20.0000 chunk 305 optimal weight: 2.9990 chunk 461 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 HIS ** D1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1051 HIS ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1068 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.076408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052187 restraints weight = 260754.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052352 restraints weight = 216219.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.052705 restraints weight = 197275.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052828 restraints weight = 189369.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052952 restraints weight = 171728.271| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 31808 Z= 0.404 Angle : 0.842 14.375 43953 Z= 0.491 Chirality : 0.046 0.278 5754 Planarity : 0.006 0.095 6132 Dihedral : 6.656 33.957 5691 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.27 % Favored : 89.72 % Rotamer: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.12), residues: 5586 helix: 1.69 (0.08), residues: 3864 sheet: 0.47 (0.31), residues: 315 loop : -2.34 (0.18), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A1082 TYR 0.013 0.001 TYR B1045 PHE 0.039 0.003 PHE F1040 TRP 0.029 0.002 TRP A 982 HIS 0.018 0.004 HIS G1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.40 (31808) covalent geometry : angle 0.84152 / 0.49 (43953) hydrogen bonds : bond 0.07441 / 5.63 ( 3299) hydrogen bonds : angle 5.69494 / 4.36 ( 9762) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 1.371 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: A 919 PHE cc_start: 0.8812 (t80) cc_final: 0.8526 (t80) REVERT: A 1034 GLN cc_start: 0.8544 (tp40) cc_final: 0.8309 (tp40) REVERT: B 919 PHE cc_start: 0.8774 (t80) cc_final: 0.8442 (t80) REVERT: B 944 ASP cc_start: 0.8462 (p0) cc_final: 0.7929 (t70) REVERT: B 1016 ARG cc_start: 0.8795 (mmp80) cc_final: 0.8370 (ttp80) REVERT: B 1034 GLN cc_start: 0.8361 (tp40) cc_final: 0.8158 (tp40) REVERT: C 1034 GLN cc_start: 0.8328 (tp40) cc_final: 0.8106 (tp40) REVERT: D 919 PHE cc_start: 0.8815 (t80) cc_final: 0.8444 (t80) REVERT: D 926 LEU cc_start: 0.9174 (mm) cc_final: 0.8619 (mm) REVERT: D 927 ILE cc_start: 0.9431 (tp) cc_final: 0.9178 (tp) REVERT: D 930 PHE cc_start: 0.7955 (m-80) cc_final: 0.7562 (m-80) REVERT: D 945 LEU cc_start: 0.9126 (mt) cc_final: 0.8854 (pp) REVERT: D 1034 GLN cc_start: 0.8726 (tp40) cc_final: 0.8346 (tp40) REVERT: E 916 GLN cc_start: 0.9039 (pm20) cc_final: 0.8742 (pm20) REVERT: E 919 PHE cc_start: 0.8878 (t80) cc_final: 0.8507 (t80) REVERT: E 944 ASP cc_start: 0.8323 (p0) cc_final: 0.7916 (t70) REVERT: E 965 LYS cc_start: 0.9116 (mptt) cc_final: 0.8810 (mmtp) REVERT: E 1034 GLN cc_start: 0.7637 (tp40) cc_final: 0.7335 (tp40) REVERT: F 932 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8721 (mmmt) REVERT: F 1034 GLN cc_start: 0.8357 (tp40) cc_final: 0.8089 (tp40) REVERT: G 944 ASP cc_start: 0.8217 (p0) cc_final: 0.7978 (t70) REVERT: G 1016 ARG cc_start: 0.8839 (mmp80) cc_final: 0.8212 (ttp80) outliers start: 2 outliers final: 0 residues processed: 373 average time/residue: 0.1598 time to fit residues: 104.5512 Evaluate side-chains 326 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 229 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 106 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 479 optimal weight: 2.9990 chunk 470 optimal weight: 0.0770 chunk 264 optimal weight: 0.0270 chunk 9 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 522 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN ** D1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1068 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056884 restraints weight = 259907.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057669 restraints weight = 206979.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.057548 restraints weight = 185484.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057763 restraints weight = 166923.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057804 restraints weight = 150841.277| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31808 Z= 0.158 Angle : 0.639 16.122 43953 Z= 0.354 Chirality : 0.043 0.181 5754 Planarity : 0.004 0.046 6132 Dihedral : 6.056 31.158 5691 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.98 % Allowed : 6.80 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.12), residues: 5586 helix: 2.11 (0.08), residues: 3857 sheet: 1.18 (0.31), residues: 315 loop : -2.47 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1082 TYR 0.007 0.001 TYR E1045 PHE 0.027 0.002 PHE C 919 TRP 0.021 0.001 TRP A 982 HIS 0.027 0.004 HIS F1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (31808) covalent geometry : angle 0.63887 / 0.35 (43953) hydrogen bonds : bond 0.04998 / 3.80 ( 3299) hydrogen bonds : angle 4.96174 / 3.79 ( 9762) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 919 PHE cc_start: 0.8637 (t80) cc_final: 0.8221 (t80) REVERT: A 923 ILE cc_start: 0.8964 (tp) cc_final: 0.8688 (tp) REVERT: A 1034 GLN cc_start: 0.8461 (tp40) cc_final: 0.7988 (tp40) REVERT: B 919 PHE cc_start: 0.8433 (t80) cc_final: 0.8030 (t80) REVERT: B 1034 GLN cc_start: 0.8072 (tp40) cc_final: 0.7798 (tp40) REVERT: B 1051 HIS cc_start: 0.6143 (t-90) cc_final: 0.5717 (t70) REVERT: C 927 ILE cc_start: 0.9157 (tp) cc_final: 0.8672 (tp) REVERT: C 930 PHE cc_start: 0.7320 (m-10) cc_final: 0.7010 (m-80) REVERT: C 931 GLU cc_start: 0.8314 (mp0) cc_final: 0.8087 (mp0) REVERT: C 945 LEU cc_start: 0.9063 (mp) cc_final: 0.8624 (pp) REVERT: D 919 PHE cc_start: 0.8504 (t80) cc_final: 0.8023 (t80) REVERT: D 923 ILE cc_start: 0.9061 (tp) cc_final: 0.8858 (tp) REVERT: D 926 LEU cc_start: 0.9060 (mm) cc_final: 0.8250 (mt) REVERT: D 927 ILE cc_start: 0.9257 (tp) cc_final: 0.9012 (tp) REVERT: D 930 PHE cc_start: 0.7635 (m-80) cc_final: 0.7236 (m-80) REVERT: D 945 LEU cc_start: 0.9093 (mt) cc_final: 0.8680 (pp) REVERT: D 1034 GLN cc_start: 0.8439 (tp40) cc_final: 0.8072 (tp40) REVERT: E 919 PHE cc_start: 0.8521 (t80) cc_final: 0.8230 (t80) REVERT: E 926 LEU cc_start: 0.8919 (mm) cc_final: 0.8024 (mm) REVERT: E 927 ILE cc_start: 0.9321 (tp) cc_final: 0.9066 (tp) REVERT: F 926 LEU cc_start: 0.8820 (mm) cc_final: 0.7638 (mm) REVERT: F 927 ILE cc_start: 0.9239 (tp) cc_final: 0.8836 (tp) REVERT: F 930 PHE cc_start: 0.7699 (m-10) cc_final: 0.7345 (m-80) REVERT: F 1016 ARG cc_start: 0.8632 (mmp80) cc_final: 0.8281 (mtt180) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1753 time to fit residues: 115.8153 Evaluate side-chains 341 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 508 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 152 optimal weight: 0.0770 chunk 110 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 433 optimal weight: 5.9990 chunk 488 optimal weight: 20.0000 chunk 428 optimal weight: 0.2980 chunk 333 optimal weight: 50.0000 chunk 494 optimal weight: 5.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1034 GLN ** F1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.081430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056738 restraints weight = 260417.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.057541 restraints weight = 207798.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057998 restraints weight = 179169.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.058183 restraints weight = 162676.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058265 restraints weight = 155249.179| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 31808 Z= 0.145 Angle : 0.603 17.855 43953 Z= 0.332 Chirality : 0.042 0.164 5754 Planarity : 0.004 0.060 6132 Dihedral : 5.591 30.806 5691 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.59 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.12), residues: 5586 helix: 2.25 (0.08), residues: 3843 sheet: 1.29 (0.30), residues: 315 loop : -2.24 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D1015 TYR 0.006 0.000 TYR B1045 PHE 0.020 0.001 PHE D 930 TRP 0.015 0.001 TRP A 982 HIS 0.026 0.004 HIS G1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (31808) covalent geometry : angle 0.60317 / 0.33 (43953) hydrogen bonds : bond 0.04451 / 3.38 ( 3299) hydrogen bonds : angle 4.64059 / 3.55 ( 9762) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11172 Ramachandran restraints generated. 5586 Oldfield, 0 Emsley, 5586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.306 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: A 919 PHE cc_start: 0.8601 (t80) cc_final: 0.8291 (t80) REVERT: A 965 LYS cc_start: 0.9279 (mmtp) cc_final: 0.9001 (mmtt) REVERT: A 1034 GLN cc_start: 0.8379 (tp40) cc_final: 0.8015 (tp40) REVERT: B 919 PHE cc_start: 0.8429 (t80) cc_final: 0.8093 (t80) REVERT: B 1051 HIS cc_start: 0.5932 (t-90) cc_final: 0.5589 (t70) REVERT: C 927 ILE cc_start: 0.9151 (tp) cc_final: 0.8773 (tp) REVERT: C 930 PHE cc_start: 0.7327 (m-10) cc_final: 0.7006 (m-80) REVERT: C 945 LEU cc_start: 0.9018 (mp) cc_final: 0.8716 (pp) REVERT: C 1053 MET cc_start: 0.8530 (mmm) cc_final: 0.8269 (mpp) REVERT: D 919 PHE cc_start: 0.8532 (t80) cc_final: 0.8009 (t80) REVERT: D 923 ILE cc_start: 0.9017 (tp) cc_final: 0.8399 (tp) REVERT: D 926 LEU cc_start: 0.9046 (mm) cc_final: 0.8080 (pp) REVERT: D 927 ILE cc_start: 0.9236 (tp) cc_final: 0.8702 (tp) REVERT: D 930 PHE cc_start: 0.7776 (m-80) cc_final: 0.7297 (m-80) REVERT: D 945 LEU cc_start: 0.9049 (mt) cc_final: 0.8755 (pp) REVERT: D 994 THR cc_start: 0.7876 (p) cc_final: 0.7527 (p) REVERT: D 1035 GLN cc_start: 0.9320 (mp10) cc_final: 0.9069 (mp10) REVERT: E 919 PHE cc_start: 0.8508 (t80) cc_final: 0.8239 (t80) REVERT: E 926 LEU cc_start: 0.8677 (mm) cc_final: 0.8432 (pp) REVERT: E 927 ILE cc_start: 0.9239 (tp) cc_final: 0.8906 (tp) REVERT: E 944 ASP cc_start: 0.8011 (p0) cc_final: 0.7763 (p0) REVERT: E 1034 GLN cc_start: 0.7294 (tp40) cc_final: 0.6976 (mm110) REVERT: F 926 LEU cc_start: 0.8745 (mm) cc_final: 0.7548 (mm) REVERT: F 927 ILE cc_start: 0.9210 (tp) cc_final: 0.8728 (tp) REVERT: F 930 PHE cc_start: 0.7649 (m-10) cc_final: 0.7298 (m-80) REVERT: F 1074 MET cc_start: 0.8215 (tpp) cc_final: 0.7880 (tpt) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.1558 time to fit residues: 106.5208 Evaluate side-chains 345 residues out of total 4788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 560 random chunks: chunk 392 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 405 optimal weight: 20.0000 chunk 293 optimal weight: 1.9990 chunk 344 optimal weight: 30.0000 chunk 366 optimal weight: 4.9990 chunk 407 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 268 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 978 GLN E1051 HIS ** E1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1060 HIS ** G 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.080995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056236 restraints weight = 260686.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056941 restraints weight = 207820.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057161 restraints weight = 180956.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057856 restraints weight = 169031.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058181 restraints weight = 157300.187| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 31808 Z= 0.148 Angle : 0.605 16.260 43953 Z= 0.334 Chirality : 0.041 0.163 5754 Planarity : 0.004 0.051 6132 Dihedral : 5.553 31.124 5691 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.02 % Favored : 92.05 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.12), residues: 5586 helix: 2.34 (0.08), residues: 3878 sheet: 1.25 (0.30), residues: 315 loop : -2.30 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1043 TYR 0.005 0.000 TYR B1045 PHE 0.042 0.002 PHE C 919 TRP 0.011 0.001 TRP A 982 HIS 0.022 0.004 HIS E1051 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (31808) covalent geometry : angle 0.60547 / 0.33 (43953) hydrogen bonds : bond 0.04547 / 3.45 ( 3299) hydrogen bonds : angle 4.55755 / 3.49 ( 9762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6067.25 seconds wall clock time: 104 minutes 27.79 seconds (6267.79 seconds total)