Starting phenix.real_space_refine on Sat Jul 4 14:13:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh5_14724/07_2026/7zh5_14724.cif" } resolution = 3.3 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= 0.001 sd= 0.009 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 114 5.16 5 C 13796 2.51 5 N 3586 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21592 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6920 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 40, 'TRANS': 863} Chain breaks: 15 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 7, 'ASN:plan1': 5, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 7018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7018 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 45, 'TRANS': 880} Chain breaks: 8 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 9, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 7332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7332 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 41, 'TRANS': 920} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 4, 'ASN:plan1': 5, 'ARG:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 3.74, per 1000 atoms: 0.17 Number of scatterers: 21592 At special positions: 0 Unit cell: (134.4, 149.1, 178.5, 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 114 16.00 O 4096 8.00 N 3586 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.05 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.04 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A 158 " " NAG A1303 " - " ASN A 227 " " NAG A1304 " - " ASN A 269 " " NAG A1305 " - " ASN A 691 " " NAG A1306 " - " ASN A 699 " " NAG A1307 " - " ASN A 783 " " NAG A1308 " - " ASN A1056 " " NAG A1309 " - " ASN A1080 " " NAG B1301 " - " ASN B 318 " " NAG B1302 " - " ASN B 602 " " NAG B1303 " - " ASN B 691 " " NAG B1304 " - " ASN B 699 " " NAG B1305 " - " ASN B 783 " " NAG B1306 " - " ASN B1056 " " NAG B1307 " - " ASN B1080 " " NAG C1301 " - " ASN C 227 " " NAG C1302 " - " ASN C 269 " " NAG C1303 " - " ASN C 602 " " NAG C1304 " - " ASN C 691 " " NAG C1305 " - " ASN C 699 " " NAG C1306 " - " ASN C 783 " " NAG C1307 " - " ASN C1056 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 933.8 milliseconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5234 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 46 sheets defined 23.4% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 370 through 377 removed outlier: 4.662A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.539A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.526A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.800A pdb=" N LEU A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.836A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.610A pdb=" N LEU A 804 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 865 removed outlier: 3.633A pdb=" N ALA A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 891 removed outlier: 3.505A pdb=" N ALA A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.516A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 970 through 1014 removed outlier: 4.079A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 370 through 377 removed outlier: 4.732A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 719 through 725 removed outlier: 3.600A pdb=" N ILE B 724 " --> pdb=" O CYS B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.580A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.876A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 889 removed outlier: 4.234A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.644A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 971 through 1014 removed outlier: 3.667A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 390 through 394 removed outlier: 3.767A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.781A pdb=" N TYR C 408 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 610 removed outlier: 3.668A pdb=" N ILE C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 724 removed outlier: 3.602A pdb=" N ILE C 724 " --> pdb=" O CYS C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.586A pdb=" N ASN C 733 " --> pdb=" O THR C 729 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.630A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.660A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 890 removed outlier: 3.665A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 889 " --> pdb=" O ALA C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 901 through 923 removed outlier: 3.683A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.629A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.681A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.761A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.003A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.867A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127 removed outlier: 4.360A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 306 removed outlier: 4.302A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 314 removed outlier: 4.053A pdb=" N VAL A 537 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 552 removed outlier: 7.234A pdb=" N PHE A 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 646 removed outlier: 5.290A pdb=" N THR A 678 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR A 644 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 694 through 710 removed outlier: 6.955A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'A' and resid 1063 through 1064 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id=AB8, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.757A pdb=" N SER B 35 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.543A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 562 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 529 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C 526 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG C 315 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.993A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.518A pdb=" N ILE B 81 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 91 Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 306 removed outlier: 4.605A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.659A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 525 through 527 Processing sheet with id=AC7, first strand: chain 'B' and resid 562 through 564 removed outlier: 3.553A pdb=" N VAL B 562 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.182A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 694 through 697 Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 710 removed outlier: 3.506A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.602A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 769 through 771 removed outlier: 3.641A pdb=" N SER C 685 " --> pdb=" O MET B 770 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.642A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B1064 " --> pdb=" O ILE B1115 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.707A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 52 through 59 removed outlier: 7.590A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 217 through 222 removed outlier: 7.167A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 123 through 128 removed outlier: 3.793A pdb=" N ARG C 126 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS C 128 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 298 through 306 removed outlier: 4.398A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 343 through 345 removed outlier: 3.941A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.276A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 695 Processing sheet with id=AE7, first strand: chain 'C' and resid 700 through 710 removed outlier: 7.189A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE9, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 4.325A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1076 through 1078 796 hydrogen bonds defined for protein. 2142 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: 3.73 Time building geometry restraints manager: 1.70 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: 3482 1.31 - 1.44: 6112 1.44 - 1.57: 12294 1.57 - 1.71: 0 1.71 - 1.84: 156 Bond restraints: 22044 Sorted by residual: bond pdb=" C PHE C 62 " pdb=" O PHE C 62 " ideal model delta sigma weight residual 1.234 1.178 0.056 1.19e-02 7.06e+03 2.24e+01 bond pdb=" N GLN C 786 " pdb=" CA GLN C 786 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.55e+01 bond pdb=" N GLU C1054 " pdb=" CA GLU C1054 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.39e+01 bond pdb=" N GLN C1053 " pdb=" CA GLN C1053 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N LYS C 793 " pdb=" CA LYS C 793 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.14e-02 7.69e+03 1.17e+01 ... (remaining 22039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 29624 2.31 - 4.62: 337 4.62 - 6.94: 14 6.94 - 9.25: 2 9.25 - 11.56: 2 Bond angle restraints: 29979 Sorted by residual: angle pdb=" CA PHE C 62 " pdb=" C PHE C 62 " pdb=" O PHE C 62 " ideal model delta sigma weight residual 121.19 109.63 11.56 1.10e+00 8.26e-01 1.10e+02 angle pdb=" O PHE C 62 " pdb=" C PHE C 62 " pdb=" N TYR C 63 " ideal model delta sigma weight residual 122.87 129.41 -6.54 1.23e+00 6.61e-01 2.82e+01 angle pdb=" N GLN C 786 " pdb=" CA GLN C 786 " pdb=" CB GLN C 786 " ideal model delta sigma weight residual 110.49 119.37 -8.88 1.69e+00 3.50e-01 2.76e+01 angle pdb=" N VAL C1110 " pdb=" CA VAL C1110 " pdb=" C VAL C1110 " ideal model delta sigma weight residual 106.21 111.57 -5.36 1.07e+00 8.73e-01 2.51e+01 angle pdb=" C GLN C1053 " pdb=" N GLU C1054 " pdb=" CA GLU C1054 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 ... (remaining 29974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 11628 17.85 - 35.71: 1057 35.71 - 53.56: 177 53.56 - 71.42: 32 71.42 - 89.27: 27 Dihedral angle restraints: 12921 sinusoidal: 4815 harmonic: 8106 Sorted by residual: dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.89 70.89 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS A 725 " pdb=" SG CYS A 725 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -149.61 63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS B 524 " pdb=" SG CYS B 524 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -26.48 -59.52 1 1.00e+01 1.00e-02 4.73e+01 ... (remaining 12918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3193 0.083 - 0.166: 330 0.166 - 0.248: 3 0.248 - 0.331: 4 0.331 - 0.414: 1 Chirality restraints: 3531 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 783 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 691 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 158 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3528 not shown) Planarity restraints: 3850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 62 " -0.017 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C PHE C 62 " 0.065 2.00e-02 2.50e+03 pdb=" O PHE C 62 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR C 63 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C1052 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C SER C1052 " 0.059 2.00e-02 2.50e+03 pdb=" O SER C1052 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN C1053 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 786 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C GLN C 786 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN C 786 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE C 787 " 0.020 2.00e-02 2.50e+03 ... (remaining 3847 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 166 2.59 - 3.17: 17652 3.17 - 3.75: 28795 3.75 - 4.32: 41876 4.32 - 4.90: 71268 Nonbonded interactions: 159757 Sorted by model distance: nonbonded pdb=" O3 NAG C1306 " pdb=" O7 NAG C1306 " model vdw 2.018 3.040 nonbonded pdb=" O3 NAG B1307 " pdb=" O7 NAG B1307 " model vdw 2.061 3.040 nonbonded pdb=" O3 NAG A1307 " pdb=" O7 NAG A1307 " model vdw 2.062 3.040 nonbonded pdb=" O LEU B 959 " pdb=" OD1 ASN B 960 " model vdw 2.184 3.040 nonbonded pdb=" O GLY A 587 " pdb=" OG1 THR A 588 " model vdw 2.197 3.040 ... (remaining 159752 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 49 or (resid 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 70 or (res \ id 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 91 or (resid 92 and (name N or name CA or name C or n \ ame O or name CB )) or resid 113 or resid 115 or resid 121 or (resid 122 and (na \ me N or name CA or name C or name O or name CB )) or resid 123 through 125 or (r \ esid 126 through 127 and (name N or name CA or name C or name O or name CB )) or \ resid 128 through 131 or resid 193 or resid 196 or resid 198 or resid 209 or (r \ esid 210 through 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 223 or (resid 224 and (name N or name CA or name C or name O \ or name CB )) or resid 225 through 228 or (resid 229 and (name N or name CA or n \ ame C or name O or name CB )) or resid 230 through 231 or (resid 232 through 233 \ and (name N or name CA or name C or name O or name CB )) or resid 234 or (resid \ 235 through 251 and (name N or name CA or name C or name O or name CB )) or res \ id 252 through 317 or resid 321 or resid 325 or (resid 328 and (name N or name C \ A or name C or name O or name CB )) or resid 342 through 347 or (resid 348 and ( \ name N or name CA or name C or name O or name CB )) or resid 349 through 366 or \ (resid 367 and (name N or name CA or name C or name O or name CB )) or resid 368 \ through 369 or (resid 370 through 371 and (name N or name CA or name C or name \ O or name CB )) or resid 372 through 379 or (resid 380 through 381 and (name N o \ r name CA or name C or name O or name CB )) or resid 382 through 384 or (resid 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or r \ esid 396 through 425 or (resid 426 through 427 and (name N or name CA or name C \ or name O or name CB )) or resid 439 through 441 or (resid 442 and (name N or na \ me CA or name C or name O or name CB )) or resid 443 or (resid 444 through 445 a \ nd (name N or name CA or name C or name O or name CB )) or resid 446 through 453 \ or resid 479 or resid 495 through 502 or (resid 503 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 through 511 or resid 517 \ through 549 or (resid 550 and (name N or name CA or name C or name O or name CB \ )) or resid 551 through 559 or (resid 560 and (name N or name CA or name C or na \ me O or name CB )) or resid 561 through 563 or (resid 564 and (name N or name CA \ or name C or name O or name CB )) or resid 565 or (resid 566 through 567 and (n \ ame N or name CA or name C or name O or name CB )) or resid 568 through 612 or ( \ resid 613 and (name N or name CA or name C or name O or name CB )) or resid 614 \ through 615 or (resid 616 and (name N or name CA or name C or name O or name CB \ )) or resid 617 through 630 or (resid 631 through 633 and (name N or name CA or \ name C or name O or name CB )) or resid 634 through 639 or (resid 640 and (name \ N or name CA or name C or name O or name CB )) or resid 641 through 642 or (resi \ d 643 and (name N or name CA or name C or name O or name CB )) or resid 644 thro \ ugh 662 or (resid 673 and (name N or name CA or name C or name O or name CB )) o \ r resid 674 through 767 or (resid 768 and (name N or name CA or name C or name O \ or name CB )) or resid 769 through 774 or (resid 775 and (name N or name CA or \ name C or name O or name CB )) or resid 776 through 792 or (resid 793 and (name \ N or name CA or name C or name O or name CB )) or resid 794 or (resid 795 and (n \ ame N or name CA or name C or name O or name CB )) or resid 796 through 811 or r \ esid 832 through 867 or (resid 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 922 or (resid 923 through 924 and (name N or na \ me CA or name C or name O or name CB )) or resid 925 through 964 or (resid 965 t \ hrough 968 and (name N or name CA or name C or name O or name CB )) or resid 969 \ or (resid 970 through 971 and (name N or name CA or name C or name O or name CB \ )) or resid 972 through 1065 or (resid 1066 and (name N or name CA or name C or \ name O or name CB )) or resid 1067 through 1073 or (resid 1074 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1075 through 1104 or (resid 11 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 1106 or (re \ sid 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 \ or (resid 1109 and (name N or name CA or name C or name O or name CB )) or resid \ 1110 through 1115 or (resid 1116 through 1119 and (name N or name CA or name C \ or name O or name CB )) or resid 1301 through 1307)) selection = (chain 'B' and (resid 32 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 49 or (resid 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 70 or resi \ d 81 through 83 or (resid 84 through 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 92 or resid 105 or resid 117 or resid 121 o \ r (resid 122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 23 through 131 or resid 138 or resid 140 or resid 142 or resid 209 or (resid 210 \ through 211 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 12 through 228 or (resid 229 and (name N or name CA or name C or name O or name \ CB )) or resid 230 through 231 or (resid 232 through 233 and (name N or name CA \ or name C or name O or name CB )) or resid 234 or (resid 235 and (name N or name \ CA or name C or name O or name CB )) or resid 251 through 317 or resid 321 or r \ esid 325 or resid 328 or resid 342 through 347 or (resid 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 350 or (resid 351 and \ (name N or name CA or name C or name O or name CB )) or resid 352 or resid 366 \ or (resid 367 and (name N or name CA or name C or name O or name CB )) or resid \ 368 through 369 or (resid 370 through 371 and (name N or name CA or name C or na \ me O or name CB )) or resid 372 through 375 or (resid 376 and (name N or name CA \ or name C or name O or name CB )) or resid 377 through 379 or (resid 380 throug \ h 381 and (name N or name CA or name C or name O or name CB )) or resid 382 thro \ ugh 396 or (resid 397 through 398 and (name N or name CA or name C or name O or \ name CB )) or resid 399 through 400 or resid 412 through 414 or (resid 415 throu \ gh 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) \ or resid 443 through 453 or resid 457 or resid 495 through 511 or resid 517 thro \ ugh 542 or (resid 543 and (name N or name CA or name C or name O or name CB )) o \ r resid 544 through 563 or (resid 564 and (name N or name CA or name C or name O \ or name CB )) or resid 565 or (resid 566 through 567 and (name N or name CA or \ name C or name O or name CB )) or resid 568 through 592 or (resid 593 and (name \ N or name CA or name C or name O or name CB )) or resid 594 through 599 or (resi \ d 600 and (name N or name CA or name C or name O or name CB )) or resid 601 or ( \ resid 602 and (name N or name CA or name C or name O or name CB )) or resid 603 \ through 629 or (resid 630 through 633 and (name N or name CA or name C or name O \ or name CB )) or resid 634 through 646 or (resid 647 and (name N or name CA or \ name C or name O or name CB )) or resid 648 through 767 or (resid 768 and (name \ N or name CA or name C or name O or name CB )) or resid 769 through 792 or (resi \ d 793 and (name N or name CA or name C or name O or name CB )) or resid 794 or ( \ resid 795 and (name N or name CA or name C or name O or name CB )) or resid 796 \ through 867 or (resid 868 and (name N or name CA or name C or name O or name CB \ )) or resid 869 through 917 or (resid 918 and (name N or name CA or name C or na \ me O or name CB )) or resid 919 through 921 or (resid 922 through 924 and (name \ N or name CA or name C or name O or name CB )) or resid 925 through 1065 or (res \ id 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 t \ hrough 1073 or (resid 1074 and (name N or name CA or name C or name O or name CB \ )) or resid 1075 through 1104 or (resid 1105 and (name N or name CA or name C o \ r name O or name CB )) or resid 1106 through 1113 or (resid 1114 and (name N or \ name CA or name C or name O or name CB )) or resid 1115 or (resid 1116 through 1 \ 119 and (name N or name CA or name C or name O or name CB )) or resid 1301 throu \ gh 1307)) selection = (chain 'C' and (resid 32 through 70 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 91 or (resid 92 and (name N or nam \ e CA or name C or name O or name CB )) or resid 113 or resid 115 or resid 121 th \ rough 125 or (resid 126 through 127 and (name N or name CA or name C or name O o \ r name CB )) or resid 128 through 130 or (resid 131 and (name N or name CA or na \ me C or name O or name CB )) or resid 193 or resid 196 or resid 198 or resid 209 \ through 210 or (resid 211 and (name N or name CA or name C or name O or name CB \ )) or resid 212 through 235 or resid 251 through 317 or resid 330 or resid 334 \ or (resid 337 and (name N or name CA or name C or name O or name CB )) or resid \ 342 through 352 or resid 366 through 384 or (resid 385 and (name N or name CA or \ name C or name O or name CB )) or resid 386 through 394 or (resid 395 and (name \ N or name CA or name C or name O or name CB )) or resid 396 through 400 or resi \ d 412 through 414 or (resid 415 through 416 and (name N or name CA or name C or \ name O or name CB )) or resid 417 through 425 or (resid 426 through 427 and (nam \ e N or name CA or name C or name O or name CB )) or resid 439 through 443 or (re \ sid 444 through 445 and (name N or name CA or name C or name O or name CB )) or \ resid 446 through 453 or resid 479 or resid 495 through 502 or (resid 503 throug \ h 506 and (name N or name CA or name C or name O or name CB )) or resid 507 thro \ ugh 542 or (resid 543 and (name N or name CA or name C or name O or name CB )) o \ r resid 544 through 549 or (resid 550 and (name N or name CA or name C or name O \ or name CB )) or resid 551 through 553 or (resid 554 and (name N or name CA or \ name C or name O or name CB )) or resid 555 through 559 or (resid 560 and (name \ N or name CA or name C or name O or name CB )) or resid 561 through 572 or (resi \ d 573 through 574 and (name N or name CA or name C or name O or name CB )) or re \ sid 575 through 592 or (resid 593 and (name N or name CA or name C or name O or \ name CB )) or resid 594 through 601 or (resid 602 and (name N or name CA or name \ C or name O or name CB )) or resid 603 through 612 or (resid 613 and (name N or \ name CA or name C or name O or name CB )) or resid 614 through 615 or (resid 61 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 617 through \ 629 or (resid 630 through 633 and (name N or name CA or name C or name O or name \ CB )) or resid 634 through 639 or (resid 640 and (name N or name CA or name C o \ r name O or name CB )) or resid 641 through 642 or (resid 643 and (name N or nam \ e CA or name C or name O or name CB )) or resid 644 through 660 or (resid 661 th \ rough 673 and (name N or name CA or name C or name O or name CB )) or resid 674 \ through 774 or (resid 775 and (name N or name CA or name C or name O or name CB \ )) or resid 776 through 917 or (resid 918 and (name N or name CA or name C or na \ me O or name CB )) or resid 919 through 921 or (resid 922 through 924 and (name \ N or name CA or name C or name O or name CB )) or resid 925 through 964 or (resi \ d 965 through 968 and (name N or name CA or name C or name O or name CB )) or re \ sid 969 or (resid 970 through 971 and (name N or name CA or name C or name O or \ name CB )) or resid 972 through 1081 or (resid 1082 and (name N or name CA or na \ me C or name O or name CB )) or resid 1083 through 1106 or (resid 1107 and (name \ N or name CA or name C or name O or name CB )) or resid 1108 or (resid 1109 and \ (name N or name CA or name C or name O or name CB )) or resid 1110 through 1113 \ or (resid 1114 and (name N or name CA or name C or name O or name CB )) or resi \ d 1115 through 1118 or (resid 1119 and (name N or name CA or name C or name O or \ name CB )) or resid 1301 through 1307)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.500 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22099 Z= 0.191 Angle : 0.614 11.561 30112 Z= 0.345 Chirality : 0.046 0.414 3531 Planarity : 0.004 0.072 3827 Dihedral : 14.134 89.270 7591 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.85 % Favored : 91.04 % Rotamer: Outliers : 0.22 % Allowed : 0.40 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.15), residues: 2724 helix: -0.72 (0.21), residues: 605 sheet: -0.50 (0.22), residues: 567 loop : -2.58 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 620 TYR 0.014 0.001 TYR A1049 PHE 0.023 0.001 PHE C 870 TRP 0.012 0.001 TRP B 868 HIS 0.007 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (22044) covalent geometry : angle 0.59722 / 0.34 (29979) SS BOND : bond 0.00457 / 0.34 ( 32) SS BOND : angle 1.44328 / 1.02 ( 64) hydrogen bonds : bond 0.27466 / 18.03 ( 796) hydrogen bonds : angle 8.73046 / 6.04 ( 2142) link_NAG-ASN : bond 0.00601 / 0.44 ( 23) link_NAG-ASN : angle 2.72371 / 1.69 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 932 ASP cc_start: 0.8053 (m-30) cc_final: 0.7793 (m-30) REVERT: B 87 ILE cc_start: 0.7827 (pt) cc_final: 0.7572 (pt) REVERT: C 219 ILE cc_start: 0.6361 (mm) cc_final: 0.5998 (tt) REVERT: C 932 ASP cc_start: 0.7126 (m-30) cc_final: 0.6807 (m-30) outliers start: 5 outliers final: 3 residues processed: 194 average time/residue: 0.1268 time to fit residues: 39.4058 Evaluate side-chains 161 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 691 ASN Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 1053 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN A 937 ASN B 692 ASN B 744 GLN C 661 HIS C1053 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161653 restraints weight = 28255.840| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 0.80 r_work: 0.3609 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3479 rms_B_bonded: 3.39 restraints_weight: 0.1250 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22099 Z= 0.151 Angle : 0.612 13.148 30112 Z= 0.319 Chirality : 0.047 0.452 3531 Planarity : 0.004 0.056 3827 Dihedral : 4.991 83.021 2974 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.00 % Favored : 91.89 % Rotamer: Outliers : 0.84 % Allowed : 5.02 % Favored : 94.14 % 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: -1.67 (0.16), residues: 2724 helix: 0.94 (0.22), residues: 621 sheet: -0.22 (0.22), residues: 541 loop : -2.45 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 620 TYR 0.018 0.001 TYR A1049 PHE 0.022 0.001 PHE C 870 TRP 0.014 0.001 TRP B 868 HIS 0.008 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (22044) covalent geometry : angle 0.58691 / 0.31 (29979) SS BOND : bond 0.00372 / 0.26 ( 32) SS BOND : angle 1.34445 / 0.95 ( 64) hydrogen bonds : bond 0.07457 / 4.79 ( 796) hydrogen bonds : angle 5.77569 / 3.93 ( 2142) link_NAG-ASN : bond 0.00722 / 0.53 ( 23) link_NAG-ASN : angle 3.44346 / 2.15 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 66 VAL cc_start: 0.8659 (p) cc_final: 0.8320 (t) REVERT: A 674 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8492 (pt) REVERT: A 932 ASP cc_start: 0.8409 (m-30) cc_final: 0.8073 (m-30) REVERT: B 87 ILE cc_start: 0.8118 (pt) cc_final: 0.7913 (pt) REVERT: B 144 MET cc_start: 0.1360 (ppp) cc_final: 0.1112 (ppp) REVERT: B 917 GLN cc_start: 0.7703 (tt0) cc_final: 0.7495 (tt0) REVERT: B 1117 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7047 (m-40) REVERT: C 219 ILE cc_start: 0.6407 (mm) cc_final: 0.6051 (tt) REVERT: C 570 ILE cc_start: 0.7433 (mp) cc_final: 0.7209 (mp) REVERT: C 932 ASP cc_start: 0.7759 (m-30) cc_final: 0.7398 (m-30) outliers start: 19 outliers final: 14 residues processed: 183 average time/residue: 0.1206 time to fit residues: 36.0220 Evaluate side-chains 174 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1117 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 1053 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 64 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 271 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 0.0770 chunk 32 optimal weight: 0.0670 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157731 restraints weight = 28534.262| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 0.77 r_work: 0.3619 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3467 rms_B_bonded: 3.84 restraints_weight: 0.1250 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22099 Z= 0.166 Angle : 0.625 13.466 30112 Z= 0.323 Chirality : 0.048 0.487 3531 Planarity : 0.005 0.062 3827 Dihedral : 5.086 76.097 2970 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 1.41 % Allowed : 8.90 % Favored : 89.69 % 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 (0.16), residues: 2724 helix: 1.33 (0.22), residues: 612 sheet: -0.19 (0.22), residues: 544 loop : -2.43 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 620 TYR 0.021 0.001 TYR A1049 PHE 0.022 0.001 PHE C 870 TRP 0.013 0.001 TRP B 868 HIS 0.009 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (22044) covalent geometry : angle 0.59990 / 0.32 (29979) SS BOND : bond 0.00424 / 0.31 ( 32) SS BOND : angle 1.51449 / 1.06 ( 64) hydrogen bonds : bond 0.06983 / 4.48 ( 796) hydrogen bonds : angle 5.42521 / 3.70 ( 2142) link_NAG-ASN : bond 0.00755 / 0.55 ( 23) link_NAG-ASN : angle 3.42528 / 2.12 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 674 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8512 (pt) REVERT: A 882 MET cc_start: 0.8487 (mtp) cc_final: 0.8252 (mtm) REVERT: A 932 ASP cc_start: 0.8412 (m-30) cc_final: 0.8175 (m-30) REVERT: B 1066 GLU cc_start: 0.6097 (pp20) cc_final: 0.5816 (pp20) REVERT: C 219 ILE cc_start: 0.6457 (mm) cc_final: 0.6027 (tt) REVERT: C 231 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.5997 (p90) REVERT: C 932 ASP cc_start: 0.7766 (m-30) cc_final: 0.7393 (m-30) outliers start: 32 outliers final: 19 residues processed: 193 average time/residue: 0.1272 time to fit residues: 39.9400 Evaluate side-chains 182 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 1053 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 148 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN B 877 GLN B 883 GLN B 917 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.148407 restraints weight = 28299.063| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.06 r_work: 0.3372 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22099 Z= 0.188 Angle : 0.652 13.677 30112 Z= 0.336 Chirality : 0.049 0.518 3531 Planarity : 0.005 0.067 3827 Dihedral : 5.287 77.641 2970 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.66 % Favored : 91.23 % Rotamer: Outliers : 1.72 % Allowed : 10.97 % Favored : 87.31 % 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: -1.63 (0.15), residues: 2724 helix: 1.31 (0.22), residues: 616 sheet: -0.41 (0.23), residues: 498 loop : -2.44 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 620 TYR 0.023 0.002 TYR A1049 PHE 0.020 0.002 PHE A 870 TRP 0.014 0.001 TRP B 868 HIS 0.010 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (22044) covalent geometry : angle 0.62713 / 0.33 (29979) SS BOND : bond 0.00481 / 0.35 ( 32) SS BOND : angle 1.73354 / 1.19 ( 64) hydrogen bonds : bond 0.07205 / 4.61 ( 796) hydrogen bonds : angle 5.37562 / 3.67 ( 2142) link_NAG-ASN : bond 0.00684 / 0.52 ( 23) link_NAG-ASN : angle 3.46043 / 2.13 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6935 (t0) REVERT: A 882 MET cc_start: 0.8522 (mtp) cc_final: 0.8301 (mtp) REVERT: A 932 ASP cc_start: 0.8423 (m-30) cc_final: 0.8190 (m-30) REVERT: B 1066 GLU cc_start: 0.6479 (pp20) cc_final: 0.6109 (pp20) REVERT: C 219 ILE cc_start: 0.6366 (mm) cc_final: 0.5990 (tt) REVERT: C 231 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.5615 (p90) REVERT: C 570 ILE cc_start: 0.7308 (mp) cc_final: 0.7032 (mp) REVERT: C 932 ASP cc_start: 0.7976 (m-30) cc_final: 0.7579 (m-30) outliers start: 39 outliers final: 30 residues processed: 191 average time/residue: 0.1311 time to fit residues: 41.2422 Evaluate side-chains 194 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 629 PHE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 1053 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 246 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 211 optimal weight: 30.0000 chunk 249 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.169352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150367 restraints weight = 28241.001| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.07 r_work: 0.3513 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22099 Z= 0.176 Angle : 0.636 13.535 30112 Z= 0.327 Chirality : 0.049 0.510 3531 Planarity : 0.005 0.067 3827 Dihedral : 5.240 77.593 2970 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.41 % Favored : 91.52 % Rotamer: Outliers : 2.42 % Allowed : 11.76 % Favored : 85.81 % 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: -1.61 (0.15), residues: 2724 helix: 1.40 (0.22), residues: 611 sheet: -0.38 (0.23), residues: 484 loop : -2.44 (0.13), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 620 TYR 0.022 0.001 TYR A1049 PHE 0.017 0.002 PHE A 870 TRP 0.011 0.001 TRP B 868 HIS 0.010 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (22044) covalent geometry : angle 0.61106 / 0.32 (29979) SS BOND : bond 0.00449 / 0.33 ( 32) SS BOND : angle 1.70735 / 1.16 ( 64) hydrogen bonds : bond 0.06905 / 4.42 ( 796) hydrogen bonds : angle 5.27565 / 3.60 ( 2142) link_NAG-ASN : bond 0.00705 / 0.53 ( 23) link_NAG-ASN : angle 3.41321 / 2.11 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 882 MET cc_start: 0.8425 (mtp) cc_final: 0.8209 (mtp) REVERT: A 932 ASP cc_start: 0.8426 (m-30) cc_final: 0.8054 (m-30) REVERT: B 416 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6485 (p90) REVERT: B 913 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 1066 GLU cc_start: 0.6488 (pp20) cc_final: 0.6168 (pp20) REVERT: C 219 ILE cc_start: 0.6329 (mm) cc_final: 0.5942 (tt) REVERT: C 231 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.5961 (p90) REVERT: C 570 ILE cc_start: 0.7488 (mp) cc_final: 0.7180 (mp) REVERT: C 932 ASP cc_start: 0.7805 (m-30) cc_final: 0.7397 (m-30) outliers start: 55 outliers final: 36 residues processed: 207 average time/residue: 0.1241 time to fit residues: 42.2476 Evaluate side-chains 200 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1064 CYS Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 1053 GLN Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 214 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 276 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 786 GLN B 692 ASN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150499 restraints weight = 28311.523| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.06 r_work: 0.3413 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22099 Z= 0.162 Angle : 0.618 13.423 30112 Z= 0.318 Chirality : 0.048 0.500 3531 Planarity : 0.005 0.064 3827 Dihedral : 5.151 78.154 2970 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.41 % Favored : 91.52 % Rotamer: Outliers : 2.51 % Allowed : 12.86 % Favored : 84.63 % 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: -1.56 (0.15), residues: 2724 helix: 1.50 (0.22), residues: 610 sheet: -0.35 (0.23), residues: 484 loop : -2.42 (0.13), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 620 TYR 0.021 0.001 TYR A1049 PHE 0.015 0.001 PHE A 527 TRP 0.010 0.001 TRP B 868 HIS 0.010 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (22044) covalent geometry : angle 0.59332 / 0.31 (29979) SS BOND : bond 0.00422 / 0.31 ( 32) SS BOND : angle 1.54364 / 1.08 ( 64) hydrogen bonds : bond 0.06628 / 4.25 ( 796) hydrogen bonds : angle 5.18972 / 3.54 ( 2142) link_NAG-ASN : bond 0.00709 / 0.53 ( 23) link_NAG-ASN : angle 3.36179 / 2.08 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASN cc_start: 0.7260 (OUTLIER) cc_final: 0.7014 (t0) REVERT: A 882 MET cc_start: 0.8400 (mtp) cc_final: 0.8191 (mtp) REVERT: A 932 ASP cc_start: 0.8358 (m-30) cc_final: 0.8127 (m-30) REVERT: A 1096 ILE cc_start: 0.7812 (mt) cc_final: 0.7489 (mt) REVERT: B 258 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7430 (ptmt) REVERT: B 416 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6333 (p90) REVERT: B 913 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (tp) REVERT: B 1066 GLU cc_start: 0.6893 (pp20) cc_final: 0.6436 (pp20) REVERT: C 219 ILE cc_start: 0.6398 (mm) cc_final: 0.5986 (tt) REVERT: C 570 ILE cc_start: 0.7417 (mp) cc_final: 0.7147 (mp) REVERT: C 932 ASP cc_start: 0.8204 (m-30) cc_final: 0.7815 (m-30) outliers start: 57 outliers final: 44 residues processed: 208 average time/residue: 0.1345 time to fit residues: 45.7651 Evaluate side-chains 207 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 629 PHE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1064 CYS Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 1053 GLN Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 246 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 692 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145761 restraints weight = 28375.334| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.13 r_work: 0.3345 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 22099 Z= 0.230 Angle : 0.702 13.958 30112 Z= 0.361 Chirality : 0.051 0.570 3531 Planarity : 0.005 0.068 3827 Dihedral : 5.544 76.562 2970 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.62 % Favored : 90.35 % Rotamer: Outliers : 2.86 % Allowed : 13.22 % Favored : 83.92 % 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: -1.79 (0.15), residues: 2724 helix: 1.15 (0.21), residues: 621 sheet: -0.38 (0.23), residues: 478 loop : -2.56 (0.13), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1001 TYR 0.025 0.002 TYR A1049 PHE 0.020 0.002 PHE A 870 TRP 0.011 0.002 TRP B 868 HIS 0.010 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (22044) covalent geometry : angle 0.67720 / 0.36 (29979) SS BOND : bond 0.00585 / 0.44 ( 32) SS BOND : angle 1.73785 / 1.23 ( 64) hydrogen bonds : bond 0.07774 / 4.98 ( 796) hydrogen bonds : angle 5.39706 / 3.69 ( 2142) link_NAG-ASN : bond 0.00709 / 0.54 ( 23) link_NAG-ASN : angle 3.59067 / 2.21 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 160 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6295 (p90) REVERT: A 347 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7079 (t0) REVERT: A 932 ASP cc_start: 0.8240 (m-30) cc_final: 0.7856 (m-30) REVERT: A 1096 ILE cc_start: 0.7802 (mt) cc_final: 0.7499 (mt) REVERT: B 416 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6252 (p90) REVERT: B 913 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8234 (tp) REVERT: B 1066 GLU cc_start: 0.6646 (pp20) cc_final: 0.6382 (pp20) REVERT: C 219 ILE cc_start: 0.6435 (mm) cc_final: 0.6022 (tt) REVERT: C 570 ILE cc_start: 0.7395 (mp) cc_final: 0.7167 (mp) REVERT: C 932 ASP cc_start: 0.7594 (m-30) cc_final: 0.7190 (m-30) outliers start: 65 outliers final: 48 residues processed: 210 average time/residue: 0.1284 time to fit residues: 44.4723 Evaluate side-chains 209 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 883 GLN Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 743 THR Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1064 CYS Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1098 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 1053 GLN Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 45 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 209 optimal weight: 30.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 614 GLN B 692 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.170771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151480 restraints weight = 28291.257| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.08 r_work: 0.3536 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22099 Z= 0.125 Angle : 0.579 13.020 30112 Z= 0.298 Chirality : 0.046 0.465 3531 Planarity : 0.004 0.062 3827 Dihedral : 4.953 78.491 2970 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.82 % Favored : 92.14 % Rotamer: Outliers : 2.38 % Allowed : 14.32 % Favored : 83.30 % 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 (0.15), residues: 2724 helix: 1.60 (0.22), residues: 615 sheet: -0.32 (0.24), residues: 466 loop : -2.38 (0.13), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 620 TYR 0.018 0.001 TYR A1049 PHE 0.013 0.001 PHE A 870 TRP 0.009 0.001 TRP B 868 HIS 0.009 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22044) covalent geometry : angle 0.55608 / 0.29 (29979) SS BOND : bond 0.00342 / 0.26 ( 32) SS BOND : angle 1.29841 / 0.92 ( 64) hydrogen bonds : bond 0.05798 / 3.73 ( 796) hydrogen bonds : angle 5.03186 / 3.43 ( 2142) link_NAG-ASN : bond 0.00720 / 0.53 ( 23) link_NAG-ASN : angle 3.21624 / 1.99 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.7085 (t0) REVERT: A 932 ASP cc_start: 0.8368 (m-30) cc_final: 0.8143 (m-30) REVERT: A 1096 ILE cc_start: 0.7869 (mt) cc_final: 0.7579 (mt) REVERT: B 258 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7262 (ptmt) REVERT: B 913 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 1066 GLU cc_start: 0.6608 (pp20) cc_final: 0.6327 (pp20) REVERT: C 219 ILE cc_start: 0.6285 (mm) cc_final: 0.5950 (tt) REVERT: C 570 ILE cc_start: 0.7351 (mp) cc_final: 0.7081 (mp) REVERT: C 932 ASP cc_start: 0.7755 (m-30) cc_final: 0.7314 (m-30) outliers start: 54 outliers final: 42 residues processed: 208 average time/residue: 0.1390 time to fit residues: 46.3713 Evaluate side-chains 202 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1100 ASP Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 974 GLN Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 1053 GLN Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 271 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 187 optimal weight: 0.0870 chunk 144 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 114 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 ASN B 692 ASN B 786 GLN B 877 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.176756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165246 restraints weight = 28163.362| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 0.78 r_work: 0.3681 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work: 0.3542 rms_B_bonded: 3.68 restraints_weight: 0.1250 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22099 Z= 0.096 Angle : 0.519 12.622 30112 Z= 0.267 Chirality : 0.045 0.389 3531 Planarity : 0.004 0.056 3827 Dihedral : 4.378 81.957 2970 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.16 % Favored : 92.80 % Rotamer: Outliers : 1.59 % Allowed : 15.20 % Favored : 83.22 % 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: -1.13 (0.16), residues: 2724 helix: 2.06 (0.22), residues: 611 sheet: 0.04 (0.24), residues: 478 loop : -2.27 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 620 TYR 0.016 0.001 TYR A1049 PHE 0.010 0.001 PHE A 89 TRP 0.008 0.001 TRP B 423 HIS 0.008 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (22044) covalent geometry : angle 0.49939 / 0.26 (29979) SS BOND : bond 0.00217 / 0.16 ( 32) SS BOND : angle 0.99241 / 0.68 ( 64) hydrogen bonds : bond 0.04172 / 2.69 ( 796) hydrogen bonds : angle 4.60503 / 3.14 ( 2142) link_NAG-ASN : bond 0.00659 / 0.48 ( 23) link_NAG-ASN : angle 2.91041 / 1.80 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7102 (t0) REVERT: A 722 MET cc_start: 0.8561 (tpt) cc_final: 0.8052 (tpt) REVERT: A 884 MET cc_start: 0.8357 (tpt) cc_final: 0.7893 (tpt) REVERT: A 932 ASP cc_start: 0.8192 (m-30) cc_final: 0.7844 (m-30) REVERT: A 1096 ILE cc_start: 0.7956 (mt) cc_final: 0.7647 (mt) REVERT: B 70 HIS cc_start: 0.5256 (m-70) cc_final: 0.4890 (m-70) REVERT: B 736 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8463 (mm) REVERT: B 801 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7164 (mt-10) REVERT: B 977 ARG cc_start: 0.6905 (mtp85) cc_final: 0.6623 (mtp85) REVERT: C 219 ILE cc_start: 0.6208 (mm) cc_final: 0.5909 (tt) REVERT: C 231 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6038 (p90) REVERT: C 256 TYR cc_start: 0.6873 (m-80) cc_final: 0.6589 (m-80) outliers start: 36 outliers final: 23 residues processed: 209 average time/residue: 0.1228 time to fit residues: 41.9146 Evaluate side-chains 188 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1053 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 40 optimal weight: 0.0030 chunk 157 optimal weight: 0.0370 chunk 189 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 274 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 627 ASN B 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.172795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.154064 restraints weight = 28331.147| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.07 r_work: 0.3423 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22099 Z= 0.118 Angle : 0.551 12.912 30112 Z= 0.282 Chirality : 0.046 0.438 3531 Planarity : 0.004 0.064 3827 Dihedral : 4.550 78.530 2970 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.89 % Favored : 92.07 % Rotamer: Outliers : 1.63 % Allowed : 15.02 % Favored : 83.35 % 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: -1.12 (0.16), residues: 2724 helix: 2.00 (0.22), residues: 613 sheet: -0.02 (0.24), residues: 473 loop : -2.21 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 620 TYR 0.019 0.001 TYR A1049 PHE 0.015 0.001 PHE A 527 TRP 0.011 0.001 TRP A 868 HIS 0.007 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22044) covalent geometry : angle 0.53037 / 0.28 (29979) SS BOND : bond 0.00292 / 0.22 ( 32) SS BOND : angle 1.18762 / 0.83 ( 64) hydrogen bonds : bond 0.05267 / 3.39 ( 796) hydrogen bonds : angle 4.72734 / 3.23 ( 2142) link_NAG-ASN : bond 0.00652 / 0.49 ( 23) link_NAG-ASN : angle 2.98893 / 1.84 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASN cc_start: 0.7174 (OUTLIER) cc_final: 0.6872 (t0) REVERT: A 884 MET cc_start: 0.8480 (tpt) cc_final: 0.7953 (tpt) REVERT: A 932 ASP cc_start: 0.8248 (m-30) cc_final: 0.7918 (m-30) REVERT: A 1096 ILE cc_start: 0.7878 (mt) cc_final: 0.7554 (mt) REVERT: B 258 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7365 (ptmt) REVERT: C 219 ILE cc_start: 0.6206 (mm) cc_final: 0.5879 (tt) REVERT: C 231 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.5608 (p90) REVERT: C 417 MET cc_start: 0.1862 (tmm) cc_final: 0.1626 (tmm) outliers start: 37 outliers final: 30 residues processed: 193 average time/residue: 0.1283 time to fit residues: 40.6246 Evaluate side-chains 187 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 958 VAL Chi-restraints excluded: chain B residue 1064 CYS Chi-restraints excluded: chain B residue 1087 THR Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1053 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 86 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN B 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.170083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.158250 restraints weight = 28408.505| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 0.78 r_work: 0.3532 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work: 0.3369 rms_B_bonded: 3.74 restraints_weight: 0.1250 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22099 Z= 0.185 Angle : 0.646 13.563 30112 Z= 0.332 Chirality : 0.049 0.519 3531 Planarity : 0.005 0.072 3827 Dihedral : 5.112 78.023 2970 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.52 % Favored : 91.45 % Rotamer: Outliers : 1.81 % Allowed : 15.02 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.16), residues: 2724 helix: 1.61 (0.21), residues: 613 sheet: -0.08 (0.23), residues: 486 loop : -2.31 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 620 TYR 0.024 0.002 TYR A1049 PHE 0.022 0.002 PHE A 527 TRP 0.012 0.001 TRP A 868 HIS 0.009 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (22044) covalent geometry : angle 0.62340 / 0.33 (29979) SS BOND : bond 0.00476 / 0.36 ( 32) SS BOND : angle 1.52057 / 1.04 ( 64) hydrogen bonds : bond 0.06924 / 4.44 ( 796) hydrogen bonds : angle 5.05197 / 3.46 ( 2142) link_NAG-ASN : bond 0.00666 / 0.50 ( 23) link_NAG-ASN : angle 3.29706 / 2.03 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4545.09 seconds wall clock time: 78 minutes 34.29 seconds (4714.29 seconds total)