Starting phenix.real_space_refine on Thu Jun 19 16:44:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d0z_27113/06_2025/8d0z_27113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d0z_27113/06_2025/8d0z_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d0z_27113/06_2025/8d0z_27113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d0z_27113/06_2025/8d0z_27113.map" model { file = "/net/cci-nas-00/data/ceres_data/8d0z_27113/06_2025/8d0z_27113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d0z_27113/06_2025/8d0z_27113.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.79, per 1000 atoms: 0.66 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: 5.34 Conformation dependent library (CDL) restraints added in 4.1 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: 3.47 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: 11.51 Time building geometry restraints manager: 6.24 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: 13435 17.71 - 35.43: 359 35.43 - 53.14: 101 53.14 - 70.85: 30 70.85 - 88.57: 14 Dihedral angle restraints: 13939 sinusoidal: 5592 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 13936 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.180 Process input model: 56.610 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 9.883 88.565 8447 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (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 TRP 0.040 0.010 TRP H 36 HIS 0.011 0.002 HIS B1083 PHE 0.046 0.006 PHE A 888 TYR 0.066 0.008 TYR B 904 ARG 0.008 0.001 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.08749 ( 11) link_NAG-ASN : angle 2.48109 ( 33) hydrogen bonds : bond 0.15925 ( 1037) hydrogen bonds : angle 8.19102 ( 2913) SS BOND : bond 0.09002 ( 36) SS BOND : angle 2.51113 ( 72) covalent geometry : bond 0.02119 (23056) covalent geometry : angle 1.78784 (31362) *********************** 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 : 2.450 Fit side-chains 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: 0.6527 (t60) REVERT: C 98 SER cc_start: 0.6900 (m) cc_final: 0.6470 (t) REVERT: C 128 ILE cc_start: 0.7390 (mt) cc_final: 0.6916 (tt) REVERT: C 229 LEU cc_start: 0.7140 (mt) cc_final: 0.6785 (mt) REVERT: C 589 PRO cc_start: 0.7976 (Cg_exo) cc_final: 0.7735 (Cg_endo) REVERT: C 756 TYR cc_start: 0.5727 (m-80) cc_final: 0.5461 (m-80) REVERT: C 869 MET cc_start: 0.8576 (mtt) cc_final: 0.8368 (mtt) REVERT: C 1029 MET cc_start: 0.8808 (tpp) cc_final: 0.8441 (tpp) REVERT: A 234 ASN cc_start: 0.5550 (m-40) cc_final: 0.4981 (t0) REVERT: A 453 TYR cc_start: 0.6929 (p90) cc_final: 0.6718 (p90) REVERT: A 495 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.6385 (p90) REVERT: A 756 TYR cc_start: 0.4976 (m-80) cc_final: 0.4731 (m-80) REVERT: A 761 THR cc_start: 0.8098 (m) cc_final: 0.7802 (t) REVERT: A 762 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7428 (mm-40) REVERT: B 129 LYS cc_start: 0.8021 (mttt) cc_final: 0.7572 (tttt) REVERT: B 227 VAL cc_start: 0.8603 (p) cc_final: 0.8371 (t) REVERT: B 241 LEU cc_start: 0.7665 (mt) cc_final: 0.7115 (mt) REVERT: B 823 PHE cc_start: 0.7154 (m-80) cc_final: 0.6951 (m-80) REVERT: H 34 MET cc_start: 0.7258 (mmm) cc_final: 0.6811 (tpp) REVERT: H 95 ASP cc_start: 0.5856 (t0) cc_final: 0.4872 (t0) outliers start: 2 outliers final: 1 residues processed: 584 average time/residue: 0.4238 time to fit residues: 368.5296 Evaluate side-chains 245 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 241 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 271 GLN C 755 GLN C 762 GLN C1054 GLN C1113 GLN C1135 ASN A 49 HIS A 121 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN 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 ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3630 r_free = 0.3630 target = 0.109269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.088226 restraints weight = 56042.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089265 restraints weight = 44774.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.089759 restraints weight = 33537.090| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23103 Z= 0.191 Angle : 0.726 8.003 31467 Z= 0.399 Chirality : 0.048 0.199 3615 Planarity : 0.005 0.048 4061 Dihedral : 5.618 30.637 3294 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.06 % Allowed : 7.88 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 2822 helix: 2.26 (0.20), residues: 615 sheet: 0.98 (0.19), residues: 684 loop : -0.28 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.006 0.001 HIS B1083 PHE 0.043 0.002 PHE A 888 TYR 0.027 0.002 TYR A 505 ARG 0.007 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 11) link_NAG-ASN : angle 2.17703 ( 33) hydrogen bonds : bond 0.05946 ( 1037) hydrogen bonds : angle 6.59320 ( 2913) SS BOND : bond 0.00836 ( 36) SS BOND : angle 1.85367 ( 72) covalent geometry : bond 0.00422 (23056) covalent geometry : angle 0.71808 (31362) *********************** 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 379 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6766 (m) cc_final: 0.6317 (t) REVERT: C 1138 TYR cc_start: 0.6897 (t80) cc_final: 0.6609 (t80) REVERT: A 228 ASP cc_start: 0.6735 (m-30) cc_final: 0.5962 (p0) REVERT: A 234 ASN cc_start: 0.5291 (m-40) cc_final: 0.4958 (t0) REVERT: A 650 LEU cc_start: 0.8763 (tp) cc_final: 0.8528 (tt) REVERT: A 752 LEU cc_start: 0.7473 (mt) cc_final: 0.6997 (tp) REVERT: A 761 THR cc_start: 0.8288 (m) cc_final: 0.8020 (t) REVERT: A 762 GLN cc_start: 0.7870 (mm110) cc_final: 0.7444 (mm-40) REVERT: B 129 LYS cc_start: 0.7890 (mttt) cc_final: 0.7380 (tttt) REVERT: B 218 GLN cc_start: 0.7218 (mt0) cc_final: 0.6565 (mp10) REVERT: B 651 ILE cc_start: 0.8535 (mm) cc_final: 0.8252 (mt) REVERT: B 957 GLN cc_start: 0.7179 (mt0) cc_final: 0.6932 (mm-40) REVERT: B 1092 GLU cc_start: 0.6941 (pp20) cc_final: 0.6559 (pp20) REVERT: H 50 ILE cc_start: 0.8296 (tt) cc_final: 0.8054 (tt) REVERT: H 58 PHE cc_start: 0.7108 (m-80) cc_final: 0.6394 (m-10) REVERT: H 83 ARG cc_start: 0.5488 (OUTLIER) cc_final: 0.5252 (ttp-110) REVERT: H 108 LEU cc_start: 0.6120 (tt) cc_final: 0.5859 (tp) outliers start: 52 outliers final: 31 residues processed: 359 average time/residue: 0.3303 time to fit residues: 187.9920 Evaluate side-chains 245 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 2.560 ------------------------------------------------------------------------------- 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 A residue 121 ASN Chi-restraints excluded: chain A residue 227 VAL 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 887 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 126 VAL 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 H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 ARG 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 123 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 147 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 265 optimal weight: 0.0470 overall best weight: 2.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS A 121 ASN A 321 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 992 GLN B 969 ASN B1048 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086606 restraints weight = 56162.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087173 restraints weight = 46620.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.087450 restraints weight = 40317.855| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 23103 Z= 0.203 Angle : 0.681 12.106 31467 Z= 0.367 Chirality : 0.047 0.218 3615 Planarity : 0.005 0.040 4061 Dihedral : 5.454 34.709 3292 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 3.25 % Allowed : 9.27 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2822 helix: 2.44 (0.20), residues: 602 sheet: 0.79 (0.18), residues: 683 loop : -0.59 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.007 0.002 HIS A1064 PHE 0.031 0.002 PHE A 888 TYR 0.027 0.002 TYR C1067 ARG 0.006 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 11) link_NAG-ASN : angle 2.17488 ( 33) hydrogen bonds : bond 0.05069 ( 1037) hydrogen bonds : angle 6.24972 ( 2913) SS BOND : bond 0.00625 ( 36) SS BOND : angle 2.10633 ( 72) covalent geometry : bond 0.00465 (23056) covalent geometry : angle 0.67083 (31362) *********************** 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 335 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6579 (m) cc_final: 0.6091 (t) REVERT: C 238 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5429 (t80) REVERT: C 614 ASP cc_start: 0.6995 (t0) cc_final: 0.6781 (t0) REVERT: A 153 MET cc_start: 0.1421 (pmm) cc_final: 0.0505 (ppp) REVERT: A 228 ASP cc_start: 0.6883 (m-30) cc_final: 0.5922 (p0) REVERT: A 234 ASN cc_start: 0.5308 (m-40) cc_final: 0.4963 (t0) REVERT: A 269 TYR cc_start: 0.6641 (m-10) cc_final: 0.6367 (m-10) REVERT: A 365 TYR cc_start: 0.8092 (m-80) cc_final: 0.7661 (m-80) REVERT: A 650 LEU cc_start: 0.8647 (tp) cc_final: 0.8412 (tt) REVERT: A 869 MET cc_start: 0.7963 (mtm) cc_final: 0.7749 (mtm) REVERT: B 129 LYS cc_start: 0.8069 (mttt) cc_final: 0.7805 (mttt) REVERT: B 207 HIS cc_start: 0.6693 (t-170) cc_final: 0.6470 (t70) REVERT: B 218 GLN cc_start: 0.7162 (mt0) cc_final: 0.6515 (mp10) REVERT: B 957 GLN cc_start: 0.7187 (mt0) cc_final: 0.6965 (mm-40) REVERT: H 86 ASP cc_start: 0.6773 (m-30) cc_final: 0.6462 (m-30) outliers start: 82 outliers final: 59 residues processed: 316 average time/residue: 0.3242 time to fit residues: 167.1784 Evaluate side-chains 258 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1128 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 323 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 432 CYS 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 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 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR 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 887 THR 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 307 THR 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 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 796 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1129 VAL 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 48 VAL 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 53 ASN 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 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 278 optimal weight: 0.0370 chunk 20 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 284 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1113 GLN A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 115 GLN B 969 ASN ** H 32 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.107880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087581 restraints weight = 56370.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088320 restraints weight = 48759.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088539 restraints weight = 38346.809| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 23103 Z= 0.135 Angle : 0.598 10.522 31467 Z= 0.320 Chirality : 0.045 0.219 3615 Planarity : 0.004 0.037 4061 Dihedral : 5.100 34.419 3292 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 2.65 % Allowed : 11.01 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 2822 helix: 2.65 (0.20), residues: 610 sheet: 0.80 (0.19), residues: 667 loop : -0.65 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.006 0.001 HIS B1083 PHE 0.021 0.001 PHE A 377 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 11) link_NAG-ASN : angle 1.94631 ( 33) hydrogen bonds : bond 0.04393 ( 1037) hydrogen bonds : angle 5.94385 ( 2913) SS BOND : bond 0.00464 ( 36) SS BOND : angle 1.73813 ( 72) covalent geometry : bond 0.00308 (23056) covalent geometry : angle 0.58949 (31362) *********************** 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 313 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6676 (m) cc_final: 0.6154 (t) REVERT: C 238 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5299 (t80) REVERT: C 591 SER cc_start: 0.6682 (OUTLIER) cc_final: 0.6469 (t) REVERT: C 602 THR cc_start: 0.8669 (p) cc_final: 0.8316 (m) REVERT: C 614 ASP cc_start: 0.6826 (t0) cc_final: 0.6400 (t0) REVERT: A 64 TRP cc_start: 0.5636 (OUTLIER) cc_final: 0.5432 (t-100) REVERT: A 136 CYS cc_start: 0.5010 (OUTLIER) cc_final: 0.4424 (t) REVERT: A 153 MET cc_start: 0.1305 (pmm) cc_final: 0.0394 (ppp) REVERT: A 887 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6873 (p) REVERT: B 129 LYS cc_start: 0.8019 (mttt) cc_final: 0.7793 (mttt) REVERT: B 218 GLN cc_start: 0.7029 (mt0) cc_final: 0.6369 (mp10) REVERT: B 651 ILE cc_start: 0.8491 (mm) cc_final: 0.8139 (mt) REVERT: H 78 LEU cc_start: 0.6498 (tp) cc_final: 0.6214 (mt) REVERT: H 108 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.5303 (pt) outliers start: 67 outliers final: 44 residues processed: 293 average time/residue: 0.3039 time to fit residues: 145.9434 Evaluate side-chains 259 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 591 SER 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 A residue 64 TRP 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 366 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 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 887 THR Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 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 978 ASN Chi-restraints excluded: chain B residue 1006 THR 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 58 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 86 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 273 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C1088 HIS A 388 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 969 ASN ** H 32 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.104733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084772 restraints weight = 56716.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085230 restraints weight = 51088.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085549 restraints weight = 45640.467| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 23103 Z= 0.235 Angle : 0.680 11.780 31467 Z= 0.363 Chirality : 0.048 0.194 3615 Planarity : 0.005 0.057 4061 Dihedral : 5.381 32.983 3292 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 3.57 % Allowed : 11.25 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2822 helix: 2.32 (0.20), residues: 609 sheet: 0.62 (0.19), residues: 690 loop : -0.94 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 64 HIS 0.008 0.002 HIS A1058 PHE 0.025 0.002 PHE B 888 TYR 0.026 0.002 TYR C1067 ARG 0.010 0.001 ARG C 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 11) link_NAG-ASN : angle 2.34440 ( 33) hydrogen bonds : bond 0.04884 ( 1037) hydrogen bonds : angle 6.09854 ( 2913) SS BOND : bond 0.00677 ( 36) SS BOND : angle 1.97688 ( 72) covalent geometry : bond 0.00555 (23056) covalent geometry : angle 0.67065 (31362) *********************** 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 317 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 227 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6476 (m) cc_final: 0.6092 (t) REVERT: C 238 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5383 (t80) REVERT: C 614 ASP cc_start: 0.6957 (t0) cc_final: 0.6557 (t0) REVERT: A 136 CYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4597 (t) REVERT: A 153 MET cc_start: 0.1748 (pmm) cc_final: 0.0770 (ppp) REVERT: A 500 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6777 (t) REVERT: B 129 LYS cc_start: 0.8090 (mttt) cc_final: 0.7878 (mttt) REVERT: B 218 GLN cc_start: 0.7211 (mt0) cc_final: 0.6501 (mp10) REVERT: B 1019 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7848 (ttm110) REVERT: H 59 TYR cc_start: 0.6593 (m-80) cc_final: 0.6329 (m-10) REVERT: H 82 ASN cc_start: 0.7906 (t0) cc_final: 0.7607 (m-40) outliers start: 90 outliers final: 65 residues processed: 298 average time/residue: 0.3133 time to fit residues: 152.7762 Evaluate side-chains 266 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 197 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL 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 998 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 120 VAL 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 385 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 480 CYS 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 604 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 1128 VAL 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 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 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 959 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 978 ASN 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 5 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 69 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS 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 73 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 143 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN B 207 HIS B 271 GLN B 969 ASN ** H 32 ASN ** 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 = 0.3598 r_free = 0.3598 target = 0.107170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087151 restraints weight = 55706.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.087979 restraints weight = 48815.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.088263 restraints weight = 40635.645| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23103 Z= 0.127 Angle : 0.586 12.209 31467 Z= 0.313 Chirality : 0.045 0.184 3615 Planarity : 0.004 0.067 4061 Dihedral : 5.042 36.516 3291 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 2.30 % Allowed : 13.11 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 2822 helix: 2.66 (0.20), residues: 605 sheet: 0.57 (0.19), residues: 684 loop : -0.81 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.005 0.001 HIS B1083 PHE 0.025 0.001 PHE A 133 TYR 0.021 0.001 TYR C1067 ARG 0.008 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 11) link_NAG-ASN : angle 1.93647 ( 33) hydrogen bonds : bond 0.04166 ( 1037) hydrogen bonds : angle 5.78127 ( 2913) SS BOND : bond 0.00418 ( 36) SS BOND : angle 1.89576 ( 72) covalent geometry : bond 0.00279 (23056) covalent geometry : angle 0.57626 (31362) *********************** 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 293 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6470 (m) cc_final: 0.6050 (t) REVERT: C 153 MET cc_start: 0.2005 (ttt) cc_final: 0.1730 (mtt) REVERT: C 238 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5491 (t80) REVERT: C 614 ASP cc_start: 0.6778 (t0) cc_final: 0.6426 (t0) REVERT: A 64 TRP cc_start: 0.5517 (OUTLIER) cc_final: 0.5169 (t60) REVERT: A 153 MET cc_start: 0.1734 (pmm) cc_final: 0.0750 (ppp) REVERT: B 129 LYS cc_start: 0.7920 (mttt) cc_final: 0.7643 (tttt) REVERT: B 218 GLN cc_start: 0.7251 (mt0) cc_final: 0.7018 (mt0) REVERT: B 651 ILE cc_start: 0.8517 (mm) cc_final: 0.8162 (mt) REVERT: H 59 TYR cc_start: 0.6586 (m-80) cc_final: 0.6363 (m-80) REVERT: L 45 VAL cc_start: 0.8023 (m) cc_final: 0.7806 (p) outliers start: 58 outliers final: 42 residues processed: 275 average time/residue: 0.3055 time to fit residues: 138.2271 Evaluate side-chains 249 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 64 TRP 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 385 THR 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 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 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1128 VAL 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 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 888 PHE Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS 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 96 VAL 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 182 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085804 restraints weight = 56311.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.085834 restraints weight = 48944.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086345 restraints weight = 47167.004| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23103 Z= 0.179 Angle : 0.620 13.391 31467 Z= 0.329 Chirality : 0.046 0.181 3615 Planarity : 0.004 0.041 4061 Dihedral : 5.085 35.623 3291 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 3.09 % Allowed : 12.64 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2822 helix: 2.59 (0.20), residues: 609 sheet: 0.48 (0.19), residues: 707 loop : -0.93 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.005 0.001 HIS A1058 PHE 0.032 0.002 PHE A 543 TYR 0.023 0.002 TYR C1067 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 11) link_NAG-ASN : angle 2.05639 ( 33) hydrogen bonds : bond 0.04366 ( 1037) hydrogen bonds : angle 5.80634 ( 2913) SS BOND : bond 0.00520 ( 36) SS BOND : angle 2.01687 ( 72) covalent geometry : bond 0.00417 (23056) covalent geometry : angle 0.60995 (31362) *********************** 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 291 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6479 (m) cc_final: 0.6067 (t) REVERT: C 173 GLN cc_start: 0.4472 (pm20) cc_final: 0.4174 (mp10) REVERT: C 238 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5553 (t80) REVERT: C 614 ASP cc_start: 0.6854 (t0) cc_final: 0.6500 (t0) REVERT: C 1127 ASP cc_start: 0.6440 (m-30) cc_final: 0.5888 (p0) REVERT: A 64 TRP cc_start: 0.5688 (OUTLIER) cc_final: 0.5243 (t60) REVERT: A 153 MET cc_start: 0.1880 (pmm) cc_final: 0.0923 (ppp) REVERT: B 129 LYS cc_start: 0.7943 (mttt) cc_final: 0.7692 (tttt) REVERT: B 218 GLN cc_start: 0.7283 (mt0) cc_final: 0.6986 (mt0) REVERT: L 45 VAL cc_start: 0.8009 (m) cc_final: 0.7786 (p) outliers start: 78 outliers final: 63 residues processed: 268 average time/residue: 0.2965 time to fit residues: 131.8887 Evaluate side-chains 269 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 204 time to evaluate : 2.677 ------------------------------------------------------------------------------- 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 998 THR Chi-restraints excluded: chain C residue 1128 VAL 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 385 THR 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 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 747 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1128 VAL 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 531 THR 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 1006 THR Chi-restraints excluded: chain H residue 5 VAL 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 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 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 147 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 214 optimal weight: 0.0970 chunk 242 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086437 restraints weight = 55867.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087277 restraints weight = 46970.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087774 restraints weight = 35826.447| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23103 Z= 0.121 Angle : 0.573 13.671 31467 Z= 0.305 Chirality : 0.044 0.184 3615 Planarity : 0.004 0.042 4061 Dihedral : 4.856 35.201 3291 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.30 % Allowed : 13.75 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 2822 helix: 2.88 (0.20), residues: 596 sheet: 0.49 (0.19), residues: 693 loop : -0.84 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 91 HIS 0.004 0.001 HIS B1083 PHE 0.028 0.001 PHE B 168 TYR 0.021 0.001 TYR B 170 ARG 0.003 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 11) link_NAG-ASN : angle 1.83321 ( 33) hydrogen bonds : bond 0.03995 ( 1037) hydrogen bonds : angle 5.64922 ( 2913) SS BOND : bond 0.00430 ( 36) SS BOND : angle 1.79328 ( 72) covalent geometry : bond 0.00270 (23056) covalent geometry : angle 0.56422 (31362) *********************** 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 285 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6528 (m) cc_final: 0.6107 (t) REVERT: C 173 GLN cc_start: 0.4558 (pm20) cc_final: 0.4226 (mp10) REVERT: C 238 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5511 (t80) REVERT: C 614 ASP cc_start: 0.6703 (t0) cc_final: 0.6290 (t0) REVERT: C 1127 ASP cc_start: 0.6321 (m-30) cc_final: 0.5838 (p0) REVERT: A 64 TRP cc_start: 0.5581 (OUTLIER) cc_final: 0.5264 (t60) REVERT: A 153 MET cc_start: 0.1709 (pmm) cc_final: 0.0742 (ppp) REVERT: B 129 LYS cc_start: 0.7953 (mttt) cc_final: 0.7567 (tttt) REVERT: B 218 GLN cc_start: 0.7341 (mt0) cc_final: 0.7064 (mt0) REVERT: B 651 ILE cc_start: 0.8559 (mm) cc_final: 0.8225 (mt) REVERT: B 1019 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8017 (ttp-170) outliers start: 58 outliers final: 52 residues processed: 266 average time/residue: 0.3071 time to fit residues: 134.9589 Evaluate side-chains 258 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1128 VAL Chi-restraints excluded: chain A residue 64 TRP 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 385 THR 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 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1128 VAL 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 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 1019 ARG Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 35 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 150 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1142 GLN A 394 ASN B 957 GLN B 969 ASN ** H 32 ASN ** 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 = 0.3571 r_free = 0.3571 target = 0.105322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085517 restraints weight = 56284.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085721 restraints weight = 47397.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085999 restraints weight = 44977.772| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23103 Z= 0.187 Angle : 0.623 14.453 31467 Z= 0.331 Chirality : 0.046 0.225 3615 Planarity : 0.004 0.041 4061 Dihedral : 5.025 32.829 3291 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 2.81 % Allowed : 13.71 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2822 helix: 2.57 (0.20), residues: 610 sheet: 0.46 (0.19), residues: 685 loop : -0.96 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.005 0.001 HIS A1058 PHE 0.021 0.002 PHE B 888 TYR 0.025 0.002 TYR B 170 ARG 0.003 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 11) link_NAG-ASN : angle 2.09112 ( 33) hydrogen bonds : bond 0.04374 ( 1037) hydrogen bonds : angle 5.79010 ( 2913) SS BOND : bond 0.00624 ( 36) SS BOND : angle 1.93088 ( 72) covalent geometry : bond 0.00437 (23056) covalent geometry : angle 0.61338 (31362) *********************** 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 273 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6448 (m) cc_final: 0.6040 (t) REVERT: C 238 PHE cc_start: 0.6252 (OUTLIER) cc_final: 0.5521 (t80) REVERT: C 614 ASP cc_start: 0.6770 (t0) cc_final: 0.6410 (t0) REVERT: C 1127 ASP cc_start: 0.6500 (m-30) cc_final: 0.5993 (p0) REVERT: A 64 TRP cc_start: 0.5690 (OUTLIER) cc_final: 0.5353 (t60) REVERT: A 153 MET cc_start: 0.1775 (pmm) cc_final: 0.0833 (ppp) REVERT: B 129 LYS cc_start: 0.7973 (mttt) cc_final: 0.7644 (tttt) REVERT: B 218 GLN cc_start: 0.7324 (mt0) cc_final: 0.6993 (mt0) REVERT: B 740 MET cc_start: 0.7986 (tpt) cc_final: 0.7785 (mmm) REVERT: B 1019 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8052 (ttp-170) outliers start: 71 outliers final: 59 residues processed: 253 average time/residue: 0.3213 time to fit residues: 133.7974 Evaluate side-chains 255 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 2.619 ------------------------------------------------------------------------------- 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 1128 VAL 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 373 SER Chi-restraints excluded: chain A residue 385 THR 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 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 604 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1128 VAL 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 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 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 1019 ARG Chi-restraints excluded: chain H residue 5 VAL 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 69 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 18 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 65 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 186 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.085536 restraints weight = 56525.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086159 restraints weight = 49101.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.086574 restraints weight = 40397.021| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 23103 Z= 0.171 Angle : 0.612 14.110 31467 Z= 0.324 Chirality : 0.046 0.217 3615 Planarity : 0.004 0.047 4061 Dihedral : 5.050 32.662 3291 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 2.73 % Allowed : 13.75 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2822 helix: 2.59 (0.20), residues: 604 sheet: 0.42 (0.19), residues: 689 loop : -1.02 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 64 HIS 0.004 0.001 HIS B1083 PHE 0.021 0.002 PHE B 888 TYR 0.024 0.002 TYR C1067 ARG 0.004 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 11) link_NAG-ASN : angle 2.12051 ( 33) hydrogen bonds : bond 0.04297 ( 1037) hydrogen bonds : angle 5.78786 ( 2913) SS BOND : bond 0.00588 ( 36) SS BOND : angle 1.88616 ( 72) covalent geometry : bond 0.00399 (23056) covalent geometry : angle 0.60237 (31362) ********************** 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 276 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 SER cc_start: 0.6440 (m) cc_final: 0.6032 (t) REVERT: C 238 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5516 (t80) REVERT: C 614 ASP cc_start: 0.6831 (t0) cc_final: 0.6464 (t0) REVERT: C 1127 ASP cc_start: 0.6466 (m-30) cc_final: 0.5975 (p0) REVERT: A 64 TRP cc_start: 0.5676 (OUTLIER) cc_final: 0.5474 (t60) REVERT: A 153 MET cc_start: 0.1900 (pmm) cc_final: 0.0937 (ppp) REVERT: B 129 LYS cc_start: 0.8006 (mttt) cc_final: 0.7670 (tttt) REVERT: B 218 GLN cc_start: 0.7259 (mt0) cc_final: 0.6988 (mt0) REVERT: B 1019 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: H 95 ASP cc_start: 0.6533 (t0) cc_final: 0.6322 (t0) outliers start: 69 outliers final: 59 residues processed: 256 average time/residue: 0.3042 time to fit residues: 128.6901 Evaluate side-chains 262 residues out of total 2524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 212 LEU 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 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 373 SER Chi-restraints excluded: chain A residue 385 THR 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 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 604 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1128 VAL 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 531 THR 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 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 1019 ARG Chi-restraints excluded: chain H residue 5 VAL 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 69 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 91 TRP 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 153 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 191 optimal weight: 0.0030 chunk 102 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086263 restraints weight = 55974.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086436 restraints weight = 51975.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086874 restraints weight = 44603.883| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23103 Z= 0.144 Angle : 0.588 13.931 31467 Z= 0.312 Chirality : 0.045 0.216 3615 Planarity : 0.004 0.042 4061 Dihedral : 4.924 31.699 3291 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 2.58 % Allowed : 14.30 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2822 helix: 2.73 (0.20), residues: 598 sheet: 0.43 (0.19), residues: 688 loop : -1.01 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 353 HIS 0.005 0.001 HIS B1083 PHE 0.028 0.001 PHE A 374 TYR 0.022 0.001 TYR C1067 ARG 0.005 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 11) link_NAG-ASN : angle 2.00172 ( 33) hydrogen bonds : bond 0.04125 ( 1037) hydrogen bonds : angle 5.71057 ( 2913) SS BOND : bond 0.00485 ( 36) SS BOND : angle 1.63805 ( 72) covalent geometry : bond 0.00333 (23056) covalent geometry : angle 0.57994 (31362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7075.86 seconds wall clock time: 123 minutes 57.97 seconds (7437.97 seconds total)