Starting phenix.real_space_refine on Sat Jul 4 18:25:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d0z_27113/07_2026/8d0z_27113.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 106 5.16 5 C 14351 2.51 5 N 3751 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s 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: 22566 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6425 Classifications: {'peptide': 824} Link IDs: {'PTRANS': 43, 'TRANS': 780} Chain breaks: 8 Chain: "A" Number of atoms: 7939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7939 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 54, 'TRANS': 960} Chain breaks: 7 Chain: "B" Number of atoms: 6395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6395 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 45, 'TRANS': 774} Chain breaks: 8 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 763 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.79, per 1000 atoms: 0.21 Number of scatterers: 22566 At special positions: 0 Unit cell: (143.165, 140.03, 214.225, 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 106 16.00 O 4358 8.00 N 3751 7.00 C 14351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS A 883 " distance=2.09 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.77 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.71 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=1.69 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 717 " " NAG B1301 " - " ASN B 717 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 331 " " NAG C1301 " - " ASN C 717 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1134 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 45 sheets defined 25.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 802 through 806 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 884 through 890 removed outlier: 3.548A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.502A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.048A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.646A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.810A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 888 No H-bonds generated for 'chain 'B' and resid 886 through 888' Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.506A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.728A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 96 through 100A Processing helix chain 'L' and resid 49 through 53 removed outlier: 4.222A pdb=" N ASN L 53 " --> pdb=" O ARG L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.761A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.116A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.515A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.895A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.387A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.284A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.620A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.390A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.441A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.441A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.829A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.416A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.441A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.725A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.804A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.422A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.247A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 354 through 355 Processing sheet with id=AC4, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.489A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.612A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.636A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.763A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.058A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.653A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.146A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.407A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.833A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.607A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.496A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.494A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.494A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.337A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.721A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.111A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.545A pdb=" N CYS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.635A pdb=" N HIS L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AE9, first strand: chain 'L' and resid 19 through 24 1075 hydrogen bonds defined for protein. 2913 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: 5.35 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4648 1.32 - 1.46: 8308 1.46 - 1.61: 9945 1.61 - 1.75: 31 1.75 - 1.90: 124 Bond restraints: 23056 Sorted by residual: bond pdb=" CB PHE A 888 " pdb=" CG PHE A 888 " ideal model delta sigma weight residual 1.502 1.300 0.202 2.30e-02 1.89e+03 7.73e+01 bond pdb=" CB HIS A1064 " pdb=" CG HIS A1064 " ideal model delta sigma weight residual 1.497 1.382 0.115 1.40e-02 5.10e+03 6.79e+01 bond pdb=" CB PHE C 55 " pdb=" CG PHE C 55 " ideal model delta sigma weight residual 1.502 1.335 0.167 2.30e-02 1.89e+03 5.27e+01 bond pdb=" CB PHE B 888 " pdb=" CG PHE B 888 " ideal model delta sigma weight residual 1.502 1.353 0.149 2.30e-02 1.89e+03 4.18e+01 bond pdb=" CB ILE C 850 " pdb=" CG1 ILE C 850 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 23051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 28184 2.86 - 5.73: 2851 5.73 - 8.59: 285 8.59 - 11.45: 39 11.45 - 14.32: 3 Bond angle restraints: 31362 Sorted by residual: angle pdb=" N ASP L 26 " pdb=" CA ASP L 26 " pdb=" C ASP L 26 " ideal model delta sigma weight residual 112.38 98.06 14.32 1.22e+00 6.72e-01 1.38e+02 angle pdb=" C THR A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta sigma weight residual 119.56 128.76 -9.20 1.02e+00 9.61e-01 8.14e+01 angle pdb=" N GLN A 613 " pdb=" CA GLN A 613 " pdb=" C GLN A 613 " ideal model delta sigma weight residual 111.28 120.73 -9.45 1.09e+00 8.42e-01 7.52e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 111.41 98.47 12.94 1.50e+00 4.44e-01 7.44e+01 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.78 128.61 -8.83 1.03e+00 9.43e-01 7.35e+01 ... (remaining 31357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13209 17.71 - 35.43: 356 35.43 - 53.14: 99 53.14 - 70.85: 30 70.85 - 88.57: 14 Dihedral angle restraints: 13708 sinusoidal: 5361 harmonic: 8347 Sorted by residual: dihedral pdb=" CB CYS A 705 " pdb=" SG CYS A 705 " pdb=" SG CYS B 883 " pdb=" CB CYS B 883 " ideal model delta sinusoidal sigma weight residual 93.00 146.44 -53.44 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C ASN L 27 " pdb=" N ASN L 27 " pdb=" CA ASN L 27 " pdb=" CB ASN L 27 " ideal model delta harmonic sigma weight residual -122.60 -110.97 -11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -119.41 33.41 1 1.00e+01 1.00e-02 1.59e+01 ... (remaining 13705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2684 0.106 - 0.212: 779 0.212 - 0.318: 116 0.318 - 0.425: 27 0.425 - 0.531: 9 Chirality restraints: 3615 Sorted by residual: chirality pdb=" CB VAL A 826 " pdb=" CA VAL A 826 " pdb=" CG1 VAL A 826 " pdb=" CG2 VAL A 826 " both_signs ideal model delta sigma weight residual False -2.63 -3.16 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CB ILE C 850 " pdb=" CA ILE C 850 " pdb=" CG1 ILE C 850 " pdb=" CG2 ILE C 850 " both_signs ideal model delta sigma weight residual False 2.64 3.15 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C2 NAG B1304 " pdb=" C1 NAG B1304 " pdb=" C3 NAG B1304 " pdb=" N2 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3612 not shown) Planarity restraints: 4072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.066 2.00e-02 2.50e+03 6.97e-02 6.08e+01 pdb=" CG ASN C 717 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " -0.043 2.00e-02 2.50e+03 4.60e-02 2.64e+01 pdb=" CG ASN B 717 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " 0.073 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 904 " -0.066 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR B 904 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 904 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 904 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 904 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 904 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 904 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 904 " -0.057 2.00e-02 2.50e+03 ... (remaining 4069 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 926 2.67 - 3.23: 21380 3.23 - 3.79: 36890 3.79 - 4.34: 49490 4.34 - 4.90: 80169 Nonbonded interactions: 188855 Sorted by model distance: nonbonded pdb=" ND2 ASN L 27 " pdb=" OE1 GLN L 31 " model vdw 2.116 3.120 nonbonded pdb=" O VAL L 28 " pdb=" N GLN L 31 " model vdw 2.320 3.120 nonbonded pdb=" N PRO L 7 " pdb=" O PRO L 7 " model vdw 2.329 2.496 nonbonded pdb=" N ASP L 26 " pdb=" N ASN L 27 " model vdw 2.357 2.560 nonbonded pdb=" C VAL L 28 " pdb=" N SER L 30 " model vdw 2.361 3.350 ... (remaining 188850 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 'B' and (resid 28 through 1144 or resid 1302 through 1304)) selection = (chain 'C' and (resid 28 through 143 or resid 154 through 331 or resid 531 throu \ gh 827 or resid 854 through 1144 or resid 1301 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.290 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.270 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.022 0.340 23103 Z= 1.145 Angle : 1.791 14.319 31467 Z= 1.221 Chirality : 0.103 0.531 3615 Planarity : 0.008 0.055 4061 Dihedral : 9.953 88.565 8216 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.08 % Allowed : 0.67 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 2822 helix: 0.73 (0.18), residues: 621 sheet: 1.28 (0.19), residues: 657 loop : 0.16 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1000 TYR 0.066 0.008 TYR B 904 PHE 0.046 0.006 PHE A 888 TRP 0.040 0.010 TRP H 36 HIS 0.011 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.02119 / 1.13 (23056) covalent geometry : angle 1.78784 / 1.22 (31362) SS BOND : bond 0.09002 / 5.50 ( 36) SS BOND : angle 2.51113 / 1.59 ( 72) hydrogen bonds : bond 0.15925 / 10.26 ( 1037) hydrogen bonds : angle 8.19102 / 5.72 ( 2913) link_NAG-ASN : bond 0.08749 / 4.20 ( 11) link_NAG-ASN : angle 2.48109 / 1.47 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 582 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 TRP cc_start: 0.6830 (t60) cc_final: 0.6528 (t60) REVERT: C 98 SER cc_start: 0.6900 (m) cc_final: 0.6460 (t) REVERT: C 128 ILE cc_start: 0.7390 (mt) cc_final: 0.6909 (tt) REVERT: C 229 LEU cc_start: 0.7140 (mt) cc_final: 0.6783 (mt) REVERT: C 589 PRO cc_start: 0.7976 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: C 756 TYR cc_start: 0.5727 (m-80) cc_final: 0.5472 (m-80) REVERT: C 869 MET cc_start: 0.8576 (mtt) cc_final: 0.8369 (mtt) REVERT: C 973 ILE cc_start: 0.7142 (pt) cc_final: 0.6817 (mt) REVERT: C 1029 MET cc_start: 0.8808 (tpp) cc_final: 0.8444 (tpp) REVERT: A 234 ASN cc_start: 0.5550 (m-40) cc_final: 0.4979 (t0) REVERT: A 353 TRP cc_start: 0.5018 (m-90) cc_final: 0.4532 (m-90) REVERT: A 453 TYR cc_start: 0.6929 (p90) cc_final: 0.6717 (p90) REVERT: A 495 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6379 (p90) REVERT: A 756 TYR cc_start: 0.4976 (m-80) cc_final: 0.4730 (m-80) REVERT: A 761 THR cc_start: 0.8098 (m) cc_final: 0.7804 (t) REVERT: A 762 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7428 (mm-40) REVERT: A 1138 TYR cc_start: 0.6540 (m-80) cc_final: 0.6226 (t80) REVERT: B 129 LYS cc_start: 0.8021 (mttt) cc_final: 0.7533 (tttt) REVERT: B 227 VAL cc_start: 0.8603 (p) cc_final: 0.8370 (t) REVERT: B 241 LEU cc_start: 0.7665 (mt) cc_final: 0.7158 (mt) REVERT: B 823 PHE cc_start: 0.7154 (m-80) cc_final: 0.6953 (m-80) REVERT: H 34 MET cc_start: 0.7258 (mmm) cc_final: 0.6809 (tpp) REVERT: H 95 ASP cc_start: 0.5856 (t0) cc_final: 0.4949 (t0) outliers start: 2 outliers final: 1 residues processed: 584 average time/residue: 0.1615 time to fit residues: 140.8154 Evaluate side-chains 243 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 ASN C 271 GLN C 762 GLN C1054 GLN C1113 GLN C1135 ASN A 49 HIS A 121 ASN A 321 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 762 GLN A 804 GLN A 914 ASN A1048 HIS B 115 GLN B 188 ASN B 239 GLN B 949 GLN ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087559 restraints weight = 56120.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088686 restraints weight = 44344.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089277 restraints weight = 32737.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089521 restraints weight = 27343.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089569 restraints weight = 25811.657| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23103 Z= 0.199 Angle : 0.732 8.736 31467 Z= 0.397 Chirality : 0.049 0.206 3615 Planarity : 0.005 0.048 4061 Dihedral : 5.739 31.973 3063 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.09 % Rotamer: Outliers : 2.34 % Allowed : 7.45 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 2822 helix: 2.18 (0.20), residues: 615 sheet: 0.89 (0.19), residues: 684 loop : -0.37 (0.14), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 31 TYR 0.029 0.002 TYR A 505 PHE 0.044 0.002 PHE A 888 TRP 0.019 0.002 TRP A 64 HIS 0.006 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (23056) covalent geometry : angle 0.72483 / 0.39 (31362) SS BOND : bond 0.00665 / 0.45 ( 36) SS BOND : angle 1.83166 / 1.02 ( 72) hydrogen bonds : bond 0.05699 / 3.62 ( 1037) hydrogen bonds : angle 6.55575 / 4.58 ( 2913) link_NAG-ASN : bond 0.00370 / 0.17 ( 11) link_NAG-ASN : angle 2.18837 / 1.29 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 325 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6720 (m) cc_final: 0.6334 (t) REVERT: C 153 MET cc_start: 0.2550 (ttt) cc_final: 0.2164 (mtt) REVERT: C 973 ILE cc_start: 0.7136 (pt) cc_final: 0.6736 (mt) REVERT: C 1113 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6557 (mp-120) REVERT: A 228 ASP cc_start: 0.6825 (m-30) cc_final: 0.5937 (p0) REVERT: A 234 ASN cc_start: 0.5288 (m-40) cc_final: 0.4928 (t0) REVERT: A 650 LEU cc_start: 0.8742 (tp) cc_final: 0.8540 (tt) REVERT: A 752 LEU cc_start: 0.7481 (mt) cc_final: 0.6977 (tp) REVERT: A 756 TYR cc_start: 0.5173 (m-80) cc_final: 0.4971 (m-80) REVERT: A 761 THR cc_start: 0.8393 (m) cc_final: 0.7796 (p) REVERT: B 129 LYS cc_start: 0.7878 (mttt) cc_final: 0.7382 (tttt) REVERT: B 218 GLN cc_start: 0.7156 (mt0) cc_final: 0.6466 (mp10) REVERT: B 651 ILE cc_start: 0.8561 (mm) cc_final: 0.8263 (mt) REVERT: B 957 GLN cc_start: 0.7167 (mt0) cc_final: 0.6939 (mm-40) REVERT: B 983 ARG cc_start: 0.6823 (mpt180) cc_final: 0.6566 (mmt-90) REVERT: B 985 ASP cc_start: 0.6674 (p0) cc_final: 0.5366 (p0) REVERT: H 58 PHE cc_start: 0.7037 (m-80) cc_final: 0.6180 (m-10) REVERT: H 83 ARG cc_start: 0.5491 (ttm-80) cc_final: 0.5244 (ttp-110) REVERT: H 108 LEU cc_start: 0.6161 (tt) cc_final: 0.5916 (tp) outliers start: 59 outliers final: 32 residues processed: 362 average time/residue: 0.1419 time to fit residues: 82.3760 Evaluate side-chains 245 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 147 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 233 optimal weight: 0.2980 chunk 143 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 87 ASN C1113 GLN A 121 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 675 GLN A 992 GLN B 188 ASN B 207 HIS B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.108214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087958 restraints weight = 56367.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088474 restraints weight = 50455.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088729 restraints weight = 41982.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089087 restraints weight = 35943.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089204 restraints weight = 33580.876| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23103 Z= 0.150 Angle : 0.630 8.015 31467 Z= 0.341 Chirality : 0.045 0.191 3615 Planarity : 0.004 0.036 4061 Dihedral : 5.320 35.541 3061 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.48 % Rotamer: Outliers : 2.34 % Allowed : 9.59 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 2822 helix: 2.49 (0.20), residues: 614 sheet: 0.86 (0.18), residues: 674 loop : -0.53 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.023 0.002 TYR C1067 PHE 0.028 0.002 PHE A 888 TRP 0.016 0.002 TRP A 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (23056) covalent geometry : angle 0.62202 / 0.34 (31362) SS BOND : bond 0.00433 / 0.26 ( 36) SS BOND : angle 1.81236 / 1.09 ( 72) hydrogen bonds : bond 0.04797 / 3.06 ( 1037) hydrogen bonds : angle 6.11149 / 4.25 ( 2913) link_NAG-ASN : bond 0.00334 / 0.16 ( 11) link_NAG-ASN : angle 1.93578 / 1.14 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6543 (m) cc_final: 0.6116 (t) REVERT: C 238 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5201 (t80) REVERT: C 602 THR cc_start: 0.8658 (p) cc_final: 0.8340 (m) REVERT: C 973 ILE cc_start: 0.7252 (pt) cc_final: 0.6832 (mt) REVERT: A 153 MET cc_start: 0.1181 (pmm) cc_final: 0.0438 (ppp) REVERT: A 228 ASP cc_start: 0.6852 (m-30) cc_final: 0.5936 (p0) REVERT: A 234 ASN cc_start: 0.5256 (m-40) cc_final: 0.4943 (t0) REVERT: A 650 LEU cc_start: 0.8616 (tp) cc_final: 0.8409 (tt) REVERT: B 129 LYS cc_start: 0.7921 (mttt) cc_final: 0.7481 (mttm) REVERT: B 218 GLN cc_start: 0.6958 (mt0) cc_final: 0.6400 (mp10) REVERT: B 651 ILE cc_start: 0.8486 (mm) cc_final: 0.8178 (mt) REVERT: B 983 ARG cc_start: 0.6923 (mpt180) cc_final: 0.6702 (mmt-90) REVERT: L 45 VAL cc_start: 0.8091 (m) cc_final: 0.7796 (p) REVERT: L 73 LEU cc_start: 0.6789 (tp) cc_final: 0.6498 (tt) REVERT: L 91 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.6522 (m100) outliers start: 59 outliers final: 40 residues processed: 308 average time/residue: 0.1399 time to fit residues: 69.2586 Evaluate side-chains 244 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 110 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 25 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS A 66 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 207 HIS B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087353 restraints weight = 56405.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087931 restraints weight = 50030.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088370 restraints weight = 39898.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088730 restraints weight = 32402.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088773 restraints weight = 31322.697| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23103 Z= 0.147 Angle : 0.595 8.247 31467 Z= 0.321 Chirality : 0.045 0.181 3615 Planarity : 0.004 0.037 4061 Dihedral : 5.092 34.329 3061 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 3.09 % Allowed : 9.87 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.15), residues: 2822 helix: 2.78 (0.20), residues: 599 sheet: 0.79 (0.19), residues: 655 loop : -0.63 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 765 TYR 0.022 0.002 TYR C1067 PHE 0.021 0.002 PHE B 168 TRP 0.018 0.002 TRP A 64 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (23056) covalent geometry : angle 0.58694 / 0.32 (31362) SS BOND : bond 0.00392 / 0.25 ( 36) SS BOND : angle 1.71680 / 1.10 ( 72) hydrogen bonds : bond 0.04377 / 2.79 ( 1037) hydrogen bonds : angle 5.88450 / 4.09 ( 2913) link_NAG-ASN : bond 0.00249 / 0.12 ( 11) link_NAG-ASN : angle 1.86237 / 1.09 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 238 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6516 (m) cc_final: 0.6189 (t) REVERT: C 237 ARG cc_start: 0.7009 (mtm180) cc_final: 0.6395 (ttp-170) REVERT: C 238 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5379 (t80) REVERT: C 592 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7129 (p90) REVERT: C 602 THR cc_start: 0.8659 (p) cc_final: 0.8343 (m) REVERT: C 983 ARG cc_start: 0.6847 (mtm-85) cc_final: 0.6494 (mtm-85) REVERT: A 64 TRP cc_start: 0.5667 (t-100) cc_final: 0.5403 (t-100) REVERT: A 136 CYS cc_start: 0.5107 (OUTLIER) cc_final: 0.4450 (t) REVERT: A 153 MET cc_start: 0.1252 (pmm) cc_final: 0.0408 (ppp) REVERT: A 228 ASP cc_start: 0.6913 (m-30) cc_final: 0.5905 (p0) REVERT: A 365 TYR cc_start: 0.8240 (m-80) cc_final: 0.7979 (m-80) REVERT: B 129 LYS cc_start: 0.8032 (mttt) cc_final: 0.7792 (mttt) REVERT: B 218 GLN cc_start: 0.7203 (mt0) cc_final: 0.6393 (mp10) REVERT: B 651 ILE cc_start: 0.8524 (mm) cc_final: 0.8191 (mt) REVERT: B 983 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6633 (mmt-90) REVERT: H 108 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.5347 (pt) outliers start: 78 outliers final: 53 residues processed: 292 average time/residue: 0.1378 time to fit residues: 65.4377 Evaluate side-chains 266 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A1064 HIS B 969 ASN B1048 HIS B1119 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084231 restraints weight = 56406.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084385 restraints weight = 50937.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084734 restraints weight = 45285.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.085071 restraints weight = 37280.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085201 restraints weight = 34336.119| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 23103 Z= 0.275 Angle : 0.726 11.909 31467 Z= 0.385 Chirality : 0.049 0.200 3615 Planarity : 0.005 0.041 4061 Dihedral : 5.592 38.870 3060 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 3.80 % Allowed : 10.90 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 2822 helix: 2.21 (0.20), residues: 610 sheet: 0.59 (0.19), residues: 670 loop : -0.97 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.027 0.002 TYR C1067 PHE 0.025 0.002 PHE B 888 TRP 0.019 0.003 TRP A 64 HIS 0.009 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 (23056) covalent geometry : angle 0.71520 / 0.38 (31362) SS BOND : bond 0.00702 / 0.41 ( 36) SS BOND : angle 2.14567 / 1.32 ( 72) hydrogen bonds : bond 0.05091 / 3.24 ( 1037) hydrogen bonds : angle 6.14472 / 4.27 ( 2913) link_NAG-ASN : bond 0.00427 / 0.21 ( 11) link_NAG-ASN : angle 2.42541 / 1.45 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 225 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6396 (m) cc_final: 0.6163 (t) REVERT: C 157 PHE cc_start: 0.4334 (OUTLIER) cc_final: 0.3539 (m-80) REVERT: C 238 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.5454 (t80) REVERT: C 592 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7214 (p90) REVERT: C 614 ASP cc_start: 0.6896 (t0) cc_final: 0.6605 (t0) REVERT: C 983 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.6218 (mtm180) REVERT: A 64 TRP cc_start: 0.5610 (OUTLIER) cc_final: 0.5192 (t60) REVERT: A 136 CYS cc_start: 0.5360 (OUTLIER) cc_final: 0.4666 (t) REVERT: A 153 MET cc_start: 0.1785 (pmm) cc_final: 0.0796 (ppp) REVERT: A 500 THR cc_start: 0.7164 (OUTLIER) cc_final: 0.6826 (t) REVERT: B 129 LYS cc_start: 0.7944 (mttt) cc_final: 0.7656 (tttt) REVERT: B 218 GLN cc_start: 0.7267 (mt0) cc_final: 0.7046 (mt0) REVERT: B 983 ARG cc_start: 0.6937 (mpt180) cc_final: 0.6686 (mmt-90) REVERT: B 1019 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7866 (ttm110) REVERT: H 33 TYR cc_start: 0.7274 (m-80) cc_final: 0.6777 (m-80) REVERT: H 58 PHE cc_start: 0.7157 (m-80) cc_final: 0.6734 (m-80) REVERT: H 82 ASN cc_start: 0.7983 (t0) cc_final: 0.7686 (m-40) outliers start: 96 outliers final: 66 residues processed: 294 average time/residue: 0.1228 time to fit residues: 59.8912 Evaluate side-chains 268 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 202 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 856 ASN C1113 GLN A 675 GLN B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.086317 restraints weight = 56493.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086444 restraints weight = 51274.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087055 restraints weight = 46622.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087290 restraints weight = 37176.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087398 restraints weight = 34151.723| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23103 Z= 0.152 Angle : 0.602 10.027 31467 Z= 0.321 Chirality : 0.045 0.175 3615 Planarity : 0.004 0.041 4061 Dihedral : 5.229 37.564 3060 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 3.09 % Allowed : 12.08 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 2822 helix: 2.52 (0.20), residues: 609 sheet: 0.61 (0.19), residues: 659 loop : -0.89 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.023 0.002 TYR C1067 PHE 0.033 0.002 PHE A 133 TRP 0.018 0.002 TRP A 64 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (23056) covalent geometry : angle 0.59244 / 0.32 (31362) SS BOND : bond 0.00403 / 0.24 ( 36) SS BOND : angle 1.92320 / 1.15 ( 72) hydrogen bonds : bond 0.04337 / 2.77 ( 1037) hydrogen bonds : angle 5.90635 / 4.11 ( 2913) link_NAG-ASN : bond 0.00296 / 0.14 ( 11) link_NAG-ASN : angle 2.06248 / 1.18 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 222 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6326 (m) cc_final: 0.6094 (t) REVERT: C 153 MET cc_start: 0.2381 (ttt) cc_final: 0.1978 (mtt) REVERT: C 157 PHE cc_start: 0.4350 (OUTLIER) cc_final: 0.3579 (m-80) REVERT: C 173 GLN cc_start: 0.6905 (mm-40) cc_final: 0.6686 (pm20) REVERT: C 238 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5532 (t80) REVERT: C 614 ASP cc_start: 0.6874 (t0) cc_final: 0.6536 (t0) REVERT: A 64 TRP cc_start: 0.5603 (OUTLIER) cc_final: 0.5319 (t60) REVERT: A 153 MET cc_start: 0.1841 (pmm) cc_final: 0.0866 (ppp) REVERT: A 430 THR cc_start: 0.6407 (m) cc_final: 0.6134 (p) REVERT: A 675 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.5032 (pp30) REVERT: B 129 LYS cc_start: 0.8025 (mttt) cc_final: 0.7693 (tttt) REVERT: B 218 GLN cc_start: 0.7257 (mt0) cc_final: 0.6632 (mt0) REVERT: B 983 ARG cc_start: 0.6906 (mpt180) cc_final: 0.6523 (mmt-90) REVERT: H 33 TYR cc_start: 0.7094 (m-80) cc_final: 0.6719 (m-80) REVERT: H 34 MET cc_start: 0.5911 (mmm) cc_final: 0.5679 (mmm) REVERT: L 45 VAL cc_start: 0.7978 (m) cc_final: 0.7767 (p) outliers start: 78 outliers final: 60 residues processed: 277 average time/residue: 0.1250 time to fit residues: 57.7845 Evaluate side-chains 263 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 98 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 220 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 204 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN A 675 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085354 restraints weight = 56293.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.085655 restraints weight = 48614.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086079 restraints weight = 47480.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086311 restraints weight = 37168.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086434 restraints weight = 34557.218| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23103 Z= 0.206 Angle : 0.640 9.437 31467 Z= 0.339 Chirality : 0.046 0.184 3615 Planarity : 0.004 0.041 4061 Dihedral : 5.304 37.174 3060 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.05 % Allowed : 12.92 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 2822 helix: 2.52 (0.20), residues: 601 sheet: 0.43 (0.19), residues: 691 loop : -0.98 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.025 0.002 TYR C1067 PHE 0.030 0.002 PHE B 168 TRP 0.018 0.003 TRP A 64 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (23056) covalent geometry : angle 0.63157 / 0.34 (31362) SS BOND : bond 0.00503 / 0.30 ( 36) SS BOND : angle 1.71982 / 1.02 ( 72) hydrogen bonds : bond 0.04539 / 2.89 ( 1037) hydrogen bonds : angle 5.96030 / 4.15 ( 2913) link_NAG-ASN : bond 0.00337 / 0.16 ( 11) link_NAG-ASN : angle 2.16825 / 1.27 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 211 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.2400 (ttt) cc_final: 0.1975 (mtt) REVERT: C 157 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.3919 (m-80) REVERT: C 238 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5526 (t80) REVERT: A 64 TRP cc_start: 0.5513 (OUTLIER) cc_final: 0.5259 (t60) REVERT: A 153 MET cc_start: 0.1908 (pmm) cc_final: 0.0933 (ppp) REVERT: A 430 THR cc_start: 0.6438 (m) cc_final: 0.6138 (p) REVERT: A 500 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6607 (t) REVERT: A 675 GLN cc_start: 0.5289 (OUTLIER) cc_final: 0.4911 (pp30) REVERT: B 129 LYS cc_start: 0.7993 (mttt) cc_final: 0.7694 (tttt) REVERT: B 218 GLN cc_start: 0.7163 (mt0) cc_final: 0.6584 (mt0) REVERT: B 983 ARG cc_start: 0.6847 (mpt180) cc_final: 0.6568 (mmt-90) REVERT: B 1019 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7751 (ttm110) REVERT: H 33 TYR cc_start: 0.7094 (m-80) cc_final: 0.6777 (m-80) outliers start: 77 outliers final: 63 residues processed: 266 average time/residue: 0.1306 time to fit residues: 56.0618 Evaluate side-chains 265 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 91 TRP Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 18 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1142 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086126 restraints weight = 56160.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086436 restraints weight = 48164.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086844 restraints weight = 48297.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087085 restraints weight = 36844.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.087227 restraints weight = 33843.670| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23103 Z= 0.165 Angle : 0.606 8.306 31467 Z= 0.322 Chirality : 0.045 0.175 3615 Planarity : 0.004 0.056 4061 Dihedral : 5.202 36.265 3060 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 3.05 % Allowed : 13.15 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2822 helix: 2.62 (0.20), residues: 595 sheet: 0.40 (0.19), residues: 698 loop : -0.99 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 995 TYR 0.023 0.002 TYR C1067 PHE 0.024 0.002 PHE C 186 TRP 0.018 0.002 TRP A 64 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (23056) covalent geometry : angle 0.59866 / 0.32 (31362) SS BOND : bond 0.00441 / 0.26 ( 36) SS BOND : angle 1.54640 / 0.93 ( 72) hydrogen bonds : bond 0.04327 / 2.76 ( 1037) hydrogen bonds : angle 5.88740 / 4.11 ( 2913) link_NAG-ASN : bond 0.00293 / 0.14 ( 11) link_NAG-ASN : angle 2.06574 / 1.20 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 216 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.2356 (ttt) cc_final: 0.1941 (mtt) REVERT: C 157 PHE cc_start: 0.4428 (OUTLIER) cc_final: 0.3906 (m-80) REVERT: C 238 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5619 (t80) REVERT: C 983 ARG cc_start: 0.6970 (ttm110) cc_final: 0.6424 (mtm110) REVERT: A 153 MET cc_start: 0.1818 (pmm) cc_final: 0.0880 (ppp) REVERT: A 430 THR cc_start: 0.6489 (m) cc_final: 0.6177 (p) REVERT: A 440 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7646 (p0) REVERT: A 500 THR cc_start: 0.6995 (OUTLIER) cc_final: 0.6785 (t) REVERT: A 869 MET cc_start: 0.7910 (mtm) cc_final: 0.7649 (mtm) REVERT: B 129 LYS cc_start: 0.8005 (mttt) cc_final: 0.7686 (tttt) REVERT: B 218 GLN cc_start: 0.7128 (mt0) cc_final: 0.6805 (mt0) REVERT: B 983 ARG cc_start: 0.6870 (mpt180) cc_final: 0.6584 (mmt-90) REVERT: B 1019 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8061 (ttp-170) REVERT: H 79 TYR cc_start: 0.5439 (m-80) cc_final: 0.5028 (m-80) REVERT: L 6 GLN cc_start: 0.7212 (tp40) cc_final: 0.6861 (tt0) outliers start: 77 outliers final: 64 residues processed: 271 average time/residue: 0.1303 time to fit residues: 58.8351 Evaluate side-chains 269 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 280 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 675 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085552 restraints weight = 56490.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085557 restraints weight = 48661.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085967 restraints weight = 45676.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.086279 restraints weight = 37190.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086402 restraints weight = 34186.516| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23103 Z= 0.188 Angle : 0.625 8.179 31467 Z= 0.331 Chirality : 0.046 0.181 3615 Planarity : 0.004 0.042 4061 Dihedral : 5.232 36.291 3060 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 3.01 % Allowed : 13.59 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 2822 helix: 2.56 (0.20), residues: 596 sheet: 0.31 (0.19), residues: 701 loop : -1.05 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.024 0.002 TYR C1067 PHE 0.024 0.002 PHE A 374 TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (23056) covalent geometry : angle 0.61761 / 0.33 (31362) SS BOND : bond 0.00522 / 0.30 ( 36) SS BOND : angle 1.57077 / 0.93 ( 72) hydrogen bonds : bond 0.04404 / 2.81 ( 1037) hydrogen bonds : angle 5.91760 / 4.14 ( 2913) link_NAG-ASN : bond 0.00320 / 0.16 ( 11) link_NAG-ASN : angle 2.16154 / 1.26 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.2365 (ttt) cc_final: 0.1911 (mtt) REVERT: C 173 GLN cc_start: 0.6051 (mp10) cc_final: 0.5694 (mp10) REVERT: C 238 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5574 (t80) REVERT: A 153 MET cc_start: 0.1941 (pmm) cc_final: 0.1046 (ppp) REVERT: A 430 THR cc_start: 0.6673 (m) cc_final: 0.6339 (p) REVERT: A 440 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7597 (p0) REVERT: A 451 TYR cc_start: 0.5673 (m-10) cc_final: 0.5441 (m-10) REVERT: A 500 THR cc_start: 0.7076 (OUTLIER) cc_final: 0.6850 (t) REVERT: B 129 LYS cc_start: 0.8029 (mttt) cc_final: 0.7750 (tttt) REVERT: B 983 ARG cc_start: 0.6959 (mpt180) cc_final: 0.6679 (mmt-90) REVERT: B 1019 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8040 (ttp-170) REVERT: H 79 TYR cc_start: 0.5400 (m-80) cc_final: 0.5040 (m-80) REVERT: L 31 GLN cc_start: 0.6610 (tt0) cc_final: 0.6300 (tt0) outliers start: 76 outliers final: 65 residues processed: 264 average time/residue: 0.1412 time to fit residues: 61.3832 Evaluate side-chains 272 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 203 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1019 ARG Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 269 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 0.4980 chunk 278 optimal weight: 0.1980 chunk 160 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 266 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 0.0060 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN A1054 GLN B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087972 restraints weight = 56477.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088328 restraints weight = 50627.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088718 restraints weight = 45592.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089006 restraints weight = 36967.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089111 restraints weight = 33380.065| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23103 Z= 0.107 Angle : 0.553 10.424 31467 Z= 0.293 Chirality : 0.044 0.181 3615 Planarity : 0.004 0.046 4061 Dihedral : 4.830 34.238 3060 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 1.78 % Allowed : 14.90 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2822 helix: 2.89 (0.20), residues: 597 sheet: 0.42 (0.19), residues: 678 loop : -0.98 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.020 0.001 TYR C1067 PHE 0.017 0.001 PHE B 592 TRP 0.021 0.002 TRP A 353 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (23056) covalent geometry : angle 0.54711 / 0.29 (31362) SS BOND : bond 0.00239 / 0.15 ( 36) SS BOND : angle 1.34396 / 0.82 ( 72) hydrogen bonds : bond 0.03814 / 2.44 ( 1037) hydrogen bonds : angle 5.63922 / 3.93 ( 2913) link_NAG-ASN : bond 0.00227 / 0.11 ( 11) link_NAG-ASN : angle 1.66464 / 0.94 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5644 Ramachandran restraints generated. 2822 Oldfield, 0 Emsley, 2822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 PHE cc_start: 0.4325 (t80) cc_final: 0.3807 (p90) REVERT: C 173 GLN cc_start: 0.5900 (mp10) cc_final: 0.5659 (mp10) REVERT: C 238 PHE cc_start: 0.6298 (OUTLIER) cc_final: 0.5619 (t80) REVERT: A 153 MET cc_start: 0.1769 (pmm) cc_final: 0.0859 (ppp) REVERT: A 430 THR cc_start: 0.6526 (m) cc_final: 0.6188 (p) REVERT: A 500 THR cc_start: 0.7267 (m) cc_final: 0.7026 (t) REVERT: B 52 GLN cc_start: 0.7801 (tp40) cc_final: 0.7583 (tp40) REVERT: B 651 ILE cc_start: 0.8560 (mm) cc_final: 0.8267 (mt) REVERT: B 1092 GLU cc_start: 0.7061 (pp20) cc_final: 0.6636 (pp20) REVERT: H 79 TYR cc_start: 0.5252 (m-80) cc_final: 0.4955 (m-80) outliers start: 45 outliers final: 38 residues processed: 270 average time/residue: 0.1410 time to fit residues: 61.0938 Evaluate side-chains 245 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 125 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 209 optimal weight: 0.0670 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 239 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 241 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 751 ASN B 969 ASN B1002 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087612 restraints weight = 56003.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088508 restraints weight = 47578.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088937 restraints weight = 36915.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089298 restraints weight = 30836.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089309 restraints weight = 28461.123| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23103 Z= 0.106 Angle : 0.551 10.212 31467 Z= 0.291 Chirality : 0.044 0.163 3615 Planarity : 0.004 0.047 4061 Dihedral : 4.668 33.428 3060 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 1.58 % Allowed : 15.37 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.15), residues: 2822 helix: 2.99 (0.20), residues: 596 sheet: 0.38 (0.19), residues: 686 loop : -0.94 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.020 0.001 TYR H 91 PHE 0.035 0.001 PHE A 374 TRP 0.027 0.002 TRP A 64 HIS 0.004 0.000 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (23056) covalent geometry : angle 0.54627 / 0.29 (31362) SS BOND : bond 0.00283 / 0.19 ( 36) SS BOND : angle 1.29051 / 0.78 ( 72) hydrogen bonds : bond 0.03726 / 2.40 ( 1037) hydrogen bonds : angle 5.55698 / 3.89 ( 2913) link_NAG-ASN : bond 0.00209 / 0.11 ( 11) link_NAG-ASN : angle 1.50021 / 0.86 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.95 seconds wall clock time: 59 minutes 38.79 seconds (3578.79 seconds total)