Starting phenix.real_space_refine on Thu Mar 5 21:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vx1_32167/03_2026/7vx1_32167.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vx1_32167/03_2026/7vx1_32167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vx1_32167/03_2026/7vx1_32167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vx1_32167/03_2026/7vx1_32167.map" model { file = "/net/cci-nas-00/data/ceres_data/7vx1_32167/03_2026/7vx1_32167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vx1_32167/03_2026/7vx1_32167.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 117 5.16 5 C 16197 2.51 5 N 4230 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25362 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Time building chain proxies: 5.84, per 1000 atoms: 0.23 Number of scatterers: 25362 At special positions: 0 Unit cell: (162.857, 150.834, 217.507, 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 117 16.00 O 4818 8.00 N 4230 7.00 C 16197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 391 " distance=2.63 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 49 sheets defined 23.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.716A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.579A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.690A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.683A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 4.259A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.930A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.307A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.607A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.559A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) 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 removed outlier: 3.957A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.692A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.213A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.589A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.563A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.843A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.731A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.104A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.568A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.783A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.959A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.304A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.570A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.598A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.845A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.026A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.180A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.579A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.959A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.503A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.951A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.675A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.780A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 882 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.058A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.592A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 3.754A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) 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 968 removed outlier: 3.961A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.627A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.440A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.321A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1154 " --> pdb=" O GLU C1150 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C1155 " --> pdb=" O GLU C1151 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C1156 " --> pdb=" O LEU C1152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C1160 " --> pdb=" O PHE C1156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.129A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.106A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.645A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.686A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.513A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.095A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.969A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.045A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.629A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.425A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.916A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.987A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.804A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 141 through 142 removed outlier: 4.397A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.587A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.055A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.687A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.642A pdb=" N VAL B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.555A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.650A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.231A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.694A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.746A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.708A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 359 removed outlier: 3.708A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.949A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.547A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.655A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 807 through 808 removed outlier: 4.520A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 944 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8189 1.34 - 1.46: 6314 1.46 - 1.58: 11306 1.58 - 1.70: 0 1.70 - 1.82: 147 Bond restraints: 25956 Sorted by residual: bond pdb=" C THR A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 1.334 1.424 -0.090 2.34e-02 1.83e+03 1.49e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.33e+00 bond pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.64e+00 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.57e+00 bond pdb=" CA THR C 531 " pdb=" C THR C 531 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.33e-02 5.65e+03 2.49e+00 ... (remaining 25951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 34835 1.61 - 3.22: 399 3.22 - 4.83: 53 4.83 - 6.44: 14 6.44 - 8.05: 3 Bond angle restraints: 35304 Sorted by residual: angle pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " ideal model delta sigma weight residual 119.52 115.80 3.72 7.90e-01 1.60e+00 2.21e+01 angle pdb=" C CYS C 361 " pdb=" CA CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sigma weight residual 116.54 111.29 5.25 1.15e+00 7.56e-01 2.08e+01 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 121.54 129.59 -8.05 1.91e+00 2.74e-01 1.78e+01 angle pdb=" N VAL B 362 " pdb=" CA VAL B 362 " pdb=" C VAL B 362 " ideal model delta sigma weight residual 108.11 113.16 -5.05 1.40e+00 5.10e-01 1.30e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.74 127.84 -5.10 1.44e+00 4.82e-01 1.26e+01 ... (remaining 35299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 15082 16.40 - 32.81: 247 32.81 - 49.21: 96 49.21 - 65.62: 15 65.62 - 82.02: 4 Dihedral angle restraints: 15444 sinusoidal: 6021 harmonic: 9423 Sorted by residual: dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " ideal model delta harmonic sigma weight residual 122.80 133.73 -10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" CA LYS C 529 " pdb=" C LYS C 529 " pdb=" N SER C 530 " pdb=" CA SER C 530 " ideal model delta harmonic sigma weight residual 180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 15441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3577 0.072 - 0.143: 398 0.143 - 0.215: 3 0.215 - 0.286: 1 0.286 - 0.358: 2 Chirality restraints: 3981 Sorted by residual: chirality pdb=" CA ASN B 360 " pdb=" N ASN B 360 " pdb=" C ASN B 360 " pdb=" CB ASN B 360 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN C 360 " pdb=" N ASN C 360 " pdb=" C ASN C 360 " pdb=" CB ASN C 360 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA ASN C 532 " pdb=" N ASN C 532 " pdb=" C ASN C 532 " pdb=" CB ASN C 532 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3978 not shown) Planarity restraints: 4581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 359 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C SER C 359 " 0.034 2.00e-02 2.50e+03 pdb=" O SER C 359 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN C 360 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 241 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C LEU A 241 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU A 241 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 245 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.022 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 479 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.020 5.00e-02 4.00e+02 ... (remaining 4578 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 49 2.38 - 3.01: 13496 3.01 - 3.64: 35752 3.64 - 4.27: 56522 4.27 - 4.90: 94359 Nonbonded interactions: 200178 Sorted by model distance: nonbonded pdb=" ND2 ASN B 360 " pdb=" OG1 THR B 523 " model vdw 1.753 3.120 nonbonded pdb=" OG1 THR C 333 " pdb=" ND2 ASN C 360 " model vdw 2.018 3.120 nonbonded pdb=" CB LEU B 335 " pdb=" O ALA B 363 " model vdw 2.083 3.440 nonbonded pdb=" O VAL B 327 " pdb=" OG1 THR B 531 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.202 3.040 ... (remaining 200173 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.890 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.598 25991 Z= 0.215 Angle : 0.512 29.884 35374 Z= 0.302 Chirality : 0.042 0.358 3981 Planarity : 0.003 0.035 4581 Dihedral : 7.462 82.019 9279 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.12), residues: 3201 helix: -2.79 (0.13), residues: 653 sheet: -0.50 (0.17), residues: 660 loop : -1.19 (0.12), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.013 0.001 TYR B 501 PHE 0.014 0.001 PHE A 32 TRP 0.014 0.001 TRP B 64 HIS 0.005 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00186 (25956) covalent geometry : angle 0.48545 (35304) SS BOND : bond 0.10112 ( 35) SS BOND : angle 3.71143 ( 70) hydrogen bonds : bond 0.25958 ( 944) hydrogen bonds : angle 9.81995 ( 2631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.4920 (m-10) cc_final: 0.4664 (m-10) REVERT: A 285 ILE cc_start: 0.5833 (mt) cc_final: 0.5373 (mt) REVERT: A 309 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5724 (mt-10) REVERT: A 417 ASN cc_start: 0.6370 (m-40) cc_final: 0.6002 (t0) REVERT: A 612 TYR cc_start: 0.6251 (m-10) cc_final: 0.5619 (m-80) REVERT: A 701 VAL cc_start: 0.8436 (t) cc_final: 0.8027 (p) REVERT: A 704 SER cc_start: 0.8352 (t) cc_final: 0.8089 (p) REVERT: A 733 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7047 (ttmt) REVERT: A 736 VAL cc_start: 0.7480 (t) cc_final: 0.7262 (t) REVERT: A 884 SER cc_start: 0.7048 (m) cc_final: 0.6694 (t) REVERT: A 933 LYS cc_start: 0.7700 (mttt) cc_final: 0.7408 (mttt) REVERT: A 955 ASN cc_start: 0.7608 (m-40) cc_final: 0.7385 (m-40) REVERT: A 1028 LYS cc_start: 0.7509 (mttt) cc_final: 0.7240 (ttmm) REVERT: A 1113 GLN cc_start: 0.7123 (mt0) cc_final: 0.6917 (mt0) REVERT: B 61 ASN cc_start: 0.7614 (m-40) cc_final: 0.6647 (p0) REVERT: B 206 LYS cc_start: 0.7613 (tptt) cc_final: 0.6940 (tptp) REVERT: B 300 LYS cc_start: 0.6417 (mttt) cc_final: 0.6007 (mttm) REVERT: B 730 SER cc_start: 0.8200 (p) cc_final: 0.7915 (m) REVERT: B 776 LYS cc_start: 0.8213 (mttt) cc_final: 0.7870 (ttmt) REVERT: B 822 LEU cc_start: 0.7642 (mt) cc_final: 0.7406 (mm) REVERT: B 864 LEU cc_start: 0.7774 (tp) cc_final: 0.7517 (tp) REVERT: B 933 LYS cc_start: 0.7787 (mttt) cc_final: 0.7476 (ttmm) REVERT: B 953 ASN cc_start: 0.7604 (m-40) cc_final: 0.7284 (m-40) REVERT: B 1084 ASP cc_start: 0.4873 (p0) cc_final: 0.4441 (p0) REVERT: B 1105 THR cc_start: 0.7791 (t) cc_final: 0.7471 (p) REVERT: C 44 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7376 (mtt90) REVERT: C 50 SER cc_start: 0.8172 (t) cc_final: 0.7956 (p) REVERT: C 117 LEU cc_start: 0.5425 (tp) cc_final: 0.4709 (mp) REVERT: C 129 LYS cc_start: 0.6257 (mttt) cc_final: 0.5569 (tppt) REVERT: C 206 LYS cc_start: 0.5776 (tptt) cc_final: 0.5223 (tttp) REVERT: C 588 THR cc_start: 0.7349 (m) cc_final: 0.7058 (t) REVERT: C 604 THR cc_start: 0.7391 (m) cc_final: 0.7154 (p) REVERT: C 704 SER cc_start: 0.8404 (t) cc_final: 0.7826 (p) REVERT: C 726 ILE cc_start: 0.7644 (mp) cc_final: 0.7327 (mt) REVERT: C 773 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5857 (mm-30) REVERT: C 922 LEU cc_start: 0.6548 (mt) cc_final: 0.6263 (mt) REVERT: C 926 GLN cc_start: 0.6441 (mm-40) cc_final: 0.5889 (tp40) REVERT: C 936 ASP cc_start: 0.7609 (m-30) cc_final: 0.7219 (m-30) REVERT: C 963 VAL cc_start: 0.7489 (t) cc_final: 0.6805 (p) REVERT: C 976 VAL cc_start: 0.7322 (t) cc_final: 0.7039 (p) REVERT: C 1029 MET cc_start: 0.7343 (tpp) cc_final: 0.6994 (tpp) REVERT: C 1048 HIS cc_start: 0.7313 (t70) cc_final: 0.6815 (t70) outliers start: 0 outliers final: 0 residues processed: 579 average time/residue: 0.1859 time to fit residues: 166.5869 Evaluate side-chains 429 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0020 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN A 474 GLN A 563 GLN A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 787 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 317 ASN B 394 ASN B 914 ASN B1058 HIS B1088 HIS B1101 HIS B1106 GLN B1108 ASN C 417 ASN C 644 GLN C 762 GLN C 824 ASN C 895 GLN C 965 GLN C1002 GLN C1011 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.229717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185185 restraints weight = 38996.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.188214 restraints weight = 21614.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192097 restraints weight = 12267.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.192542 restraints weight = 8810.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.191820 restraints weight = 7801.129| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 25991 Z= 0.198 Angle : 0.614 9.970 35374 Z= 0.326 Chirality : 0.047 0.191 3981 Planarity : 0.005 0.060 4581 Dihedral : 4.305 22.307 3468 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.38 % Allowed : 5.19 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3201 helix: -0.16 (0.18), residues: 706 sheet: -0.30 (0.17), residues: 675 loop : -1.12 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.019 0.002 TYR B 265 PHE 0.029 0.002 PHE B1075 TRP 0.018 0.001 TRP C 64 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00434 (25956) covalent geometry : angle 0.60813 (35304) SS BOND : bond 0.00885 ( 35) SS BOND : angle 2.01882 ( 70) hydrogen bonds : bond 0.04872 ( 944) hydrogen bonds : angle 6.32344 ( 2631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 462 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.7261 (mttt) cc_final: 0.6916 (mttp) REVERT: A 304 LYS cc_start: 0.7904 (mmmm) cc_final: 0.7544 (mmtm) REVERT: A 417 ASN cc_start: 0.6594 (m-40) cc_final: 0.6214 (t0) REVERT: A 535 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8625 (mttt) REVERT: A 568 ASP cc_start: 0.6834 (p0) cc_final: 0.6478 (p0) REVERT: A 569 ILE cc_start: 0.8204 (mt) cc_final: 0.7984 (mt) REVERT: A 583 GLU cc_start: 0.4629 (mt-10) cc_final: 0.4421 (mt-10) REVERT: A 615 VAL cc_start: 0.6169 (p) cc_final: 0.5800 (m) REVERT: A 671 CYS cc_start: 0.4371 (p) cc_final: 0.3867 (p) REVERT: A 675 GLN cc_start: 0.7207 (mp10) cc_final: 0.6934 (mp10) REVERT: A 704 SER cc_start: 0.8408 (t) cc_final: 0.8006 (p) REVERT: A 748 GLU cc_start: 0.6232 (mt-10) cc_final: 0.6018 (mp0) REVERT: A 1017 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: A 1028 LYS cc_start: 0.7752 (mttt) cc_final: 0.7362 (ttmm) REVERT: A 1072 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: A 1105 THR cc_start: 0.8113 (t) cc_final: 0.7741 (m) REVERT: A 1139 ASP cc_start: 0.7547 (t0) cc_final: 0.7219 (t0) REVERT: B 206 LYS cc_start: 0.7769 (tptt) cc_final: 0.7550 (tptp) REVERT: B 302 THR cc_start: 0.7814 (m) cc_final: 0.7480 (t) REVERT: B 394 ASN cc_start: 0.7068 (m110) cc_final: 0.6115 (t0) REVERT: B 536 ASN cc_start: 0.8133 (t0) cc_final: 0.7899 (t0) REVERT: B 703 ASN cc_start: 0.7942 (t0) cc_final: 0.7706 (p0) REVERT: B 724 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 741 TYR cc_start: 0.7073 (t80) cc_final: 0.6562 (t80) REVERT: B 748 GLU cc_start: 0.6419 (mp0) cc_final: 0.6218 (mp0) REVERT: B 775 ASP cc_start: 0.7061 (m-30) cc_final: 0.6830 (m-30) REVERT: B 776 LYS cc_start: 0.8290 (mttt) cc_final: 0.7842 (ttmt) REVERT: B 933 LYS cc_start: 0.7922 (mttt) cc_final: 0.7636 (ttmm) REVERT: B 953 ASN cc_start: 0.7784 (m-40) cc_final: 0.7570 (m-40) REVERT: B 1028 LYS cc_start: 0.7371 (mtmm) cc_final: 0.7046 (mttm) REVERT: B 1105 THR cc_start: 0.8010 (t) cc_final: 0.7695 (p) REVERT: C 31 SER cc_start: 0.6096 (OUTLIER) cc_final: 0.5566 (m) REVERT: C 58 PHE cc_start: 0.6427 (m-10) cc_final: 0.6188 (m-10) REVERT: C 117 LEU cc_start: 0.6157 (tp) cc_final: 0.4991 (mp) REVERT: C 588 THR cc_start: 0.7688 (m) cc_final: 0.7405 (t) REVERT: C 604 THR cc_start: 0.7613 (m) cc_final: 0.7347 (p) REVERT: C 773 GLU cc_start: 0.6254 (mm-30) cc_final: 0.5957 (mm-30) REVERT: C 936 ASP cc_start: 0.7379 (m-30) cc_final: 0.7176 (m-30) REVERT: C 963 VAL cc_start: 0.7735 (t) cc_final: 0.7020 (p) REVERT: C 994 ASP cc_start: 0.6425 (m-30) cc_final: 0.5974 (m-30) REVERT: C 1029 MET cc_start: 0.7518 (tpp) cc_final: 0.7189 (tpp) REVERT: C 1034 LEU cc_start: 0.6639 (tt) cc_final: 0.6275 (mp) REVERT: C 1048 HIS cc_start: 0.7194 (t70) cc_final: 0.6771 (t70) outliers start: 39 outliers final: 21 residues processed: 481 average time/residue: 0.1821 time to fit residues: 136.1255 Evaluate side-chains 427 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 402 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 105 optimal weight: 0.0870 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 319 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 182 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 955 ASN A1005 GLN A1023 ASN B 66 HIS B 824 ASN B1134 ASN C 239 GLN C 317 ASN C 321 GLN C1108 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.227862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.181586 restraints weight = 40126.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.182920 restraints weight = 22774.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.185743 restraints weight = 15177.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.186686 restraints weight = 11240.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.186550 restraints weight = 9723.515| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25991 Z= 0.134 Angle : 0.538 8.857 35374 Z= 0.281 Chirality : 0.044 0.172 3981 Planarity : 0.004 0.058 4581 Dihedral : 4.155 22.237 3468 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.24 % Allowed : 7.38 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 3201 helix: 0.66 (0.19), residues: 704 sheet: -0.07 (0.18), residues: 692 loop : -1.04 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 815 TYR 0.019 0.001 TYR C 160 PHE 0.018 0.002 PHE B1075 TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00288 (25956) covalent geometry : angle 0.53416 (35304) SS BOND : bond 0.00383 ( 35) SS BOND : angle 1.61446 ( 70) hydrogen bonds : bond 0.04193 ( 944) hydrogen bonds : angle 5.68419 ( 2631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 427 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 LYS cc_start: 0.7842 (mmmm) cc_final: 0.7501 (mmtm) REVERT: A 313 TYR cc_start: 0.7493 (m-80) cc_final: 0.7021 (m-80) REVERT: A 417 ASN cc_start: 0.6692 (m-40) cc_final: 0.6286 (t0) REVERT: A 604 THR cc_start: 0.7318 (m) cc_final: 0.7118 (m) REVERT: A 699 LEU cc_start: 0.8004 (mt) cc_final: 0.7754 (mp) REVERT: A 702 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6169 (tm-30) REVERT: A 704 SER cc_start: 0.8396 (t) cc_final: 0.8024 (p) REVERT: A 775 ASP cc_start: 0.7957 (m-30) cc_final: 0.6917 (t0) REVERT: A 965 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7475 (mm-40) REVERT: A 1017 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: A 1028 LYS cc_start: 0.7876 (mttt) cc_final: 0.7401 (ttmm) REVERT: A 1029 MET cc_start: 0.7598 (tpp) cc_final: 0.7329 (tpp) REVERT: A 1039 ARG cc_start: 0.6726 (mtp180) cc_final: 0.6411 (ttp-110) REVERT: A 1139 ASP cc_start: 0.7430 (t0) cc_final: 0.7073 (t0) REVERT: B 160 TYR cc_start: 0.6802 (m-80) cc_final: 0.6516 (m-80) REVERT: B 191 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7053 (mt-10) REVERT: B 195 LYS cc_start: 0.6424 (pttt) cc_final: 0.5475 (ttpt) REVERT: B 201 PHE cc_start: 0.6185 (m-10) cc_final: 0.5898 (m-10) REVERT: B 302 THR cc_start: 0.7695 (m) cc_final: 0.7493 (t) REVERT: B 536 ASN cc_start: 0.8361 (t0) cc_final: 0.8078 (t0) REVERT: B 703 ASN cc_start: 0.7942 (t0) cc_final: 0.7664 (p0) REVERT: B 724 THR cc_start: 0.7798 (m) cc_final: 0.7388 (p) REVERT: B 765 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6789 (mtt180) REVERT: B 776 LYS cc_start: 0.8309 (mttt) cc_final: 0.8016 (ttmt) REVERT: B 790 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7408 (mmtp) REVERT: B 864 LEU cc_start: 0.8001 (tp) cc_final: 0.7705 (tp) REVERT: B 933 LYS cc_start: 0.7796 (mttt) cc_final: 0.7583 (mmmm) REVERT: B 1105 THR cc_start: 0.7981 (t) cc_final: 0.7638 (p) REVERT: C 31 SER cc_start: 0.5993 (OUTLIER) cc_final: 0.5510 (m) REVERT: C 58 PHE cc_start: 0.6443 (m-10) cc_final: 0.6190 (m-10) REVERT: C 59 PHE cc_start: 0.7185 (m-10) cc_final: 0.6766 (m-80) REVERT: C 285 ILE cc_start: 0.7628 (mt) cc_final: 0.7367 (mt) REVERT: C 588 THR cc_start: 0.7657 (m) cc_final: 0.7287 (t) REVERT: C 655 HIS cc_start: 0.6801 (t-90) cc_final: 0.6373 (t70) REVERT: C 773 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6039 (mm-30) REVERT: C 776 LYS cc_start: 0.7750 (tttt) cc_final: 0.7531 (tttt) REVERT: C 854 LYS cc_start: 0.6517 (mtpt) cc_final: 0.6093 (mtpt) REVERT: C 868 GLU cc_start: 0.7898 (tp30) cc_final: 0.7593 (tp30) REVERT: C 963 VAL cc_start: 0.7759 (t) cc_final: 0.7004 (p) REVERT: C 994 ASP cc_start: 0.6439 (m-30) cc_final: 0.6040 (m-30) REVERT: C 1029 MET cc_start: 0.7625 (tpp) cc_final: 0.7077 (tpp) REVERT: C 1048 HIS cc_start: 0.7312 (t70) cc_final: 0.6806 (t70) outliers start: 35 outliers final: 18 residues processed: 447 average time/residue: 0.1892 time to fit residues: 131.0557 Evaluate side-chains 418 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 398 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 214 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 96 optimal weight: 0.1980 chunk 270 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A1088 HIS B 644 GLN B 787 GLN B 824 ASN B1134 ASN C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.224052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.180017 restraints weight = 39658.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.179730 restraints weight = 25242.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181455 restraints weight = 16822.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.182241 restraints weight = 13961.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.182221 restraints weight = 12156.238| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25991 Z= 0.167 Angle : 0.568 9.523 35374 Z= 0.297 Chirality : 0.045 0.211 3981 Planarity : 0.005 0.128 4581 Dihedral : 4.376 22.819 3468 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.87 % Allowed : 8.65 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3201 helix: 0.77 (0.19), residues: 713 sheet: -0.04 (0.18), residues: 696 loop : -1.03 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.023 0.001 TYR C 789 PHE 0.025 0.002 PHE A 906 TRP 0.012 0.001 TRP B1102 HIS 0.007 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00363 (25956) covalent geometry : angle 0.56281 (35304) SS BOND : bond 0.00479 ( 35) SS BOND : angle 1.78925 ( 70) hydrogen bonds : bond 0.04074 ( 944) hydrogen bonds : angle 5.45891 ( 2631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 429 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.6318 (mt) cc_final: 0.5968 (mt) REVERT: A 304 LYS cc_start: 0.7883 (mmmm) cc_final: 0.7567 (mmtm) REVERT: A 417 ASN cc_start: 0.6859 (m-40) cc_final: 0.6491 (t0) REVERT: A 534 VAL cc_start: 0.8079 (t) cc_final: 0.7827 (m) REVERT: A 699 LEU cc_start: 0.8041 (mt) cc_final: 0.7765 (mp) REVERT: A 704 SER cc_start: 0.8526 (t) cc_final: 0.8090 (p) REVERT: A 737 ASP cc_start: 0.7031 (t70) cc_final: 0.6443 (t70) REVERT: A 965 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7519 (mm-40) REVERT: A 1017 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: A 1029 MET cc_start: 0.7713 (tpp) cc_final: 0.7317 (tpp) REVERT: A 1139 ASP cc_start: 0.7584 (t0) cc_final: 0.7241 (t0) REVERT: B 51 THR cc_start: 0.7834 (t) cc_final: 0.7580 (p) REVERT: B 195 LYS cc_start: 0.6703 (pttt) cc_final: 0.5822 (ttpt) REVERT: B 201 PHE cc_start: 0.6455 (m-10) cc_final: 0.6111 (m-10) REVERT: B 302 THR cc_start: 0.7782 (m) cc_final: 0.7542 (t) REVERT: B 692 ILE cc_start: 0.6746 (mt) cc_final: 0.6405 (mt) REVERT: B 703 ASN cc_start: 0.8028 (t0) cc_final: 0.7724 (p0) REVERT: B 776 LYS cc_start: 0.8326 (mttt) cc_final: 0.8058 (ttmt) REVERT: B 822 LEU cc_start: 0.7837 (mp) cc_final: 0.7540 (mm) REVERT: B 861 LEU cc_start: 0.8846 (mm) cc_final: 0.8631 (mt) REVERT: B 933 LYS cc_start: 0.7841 (mttt) cc_final: 0.7532 (ttmm) REVERT: B 950 ASP cc_start: 0.6440 (m-30) cc_final: 0.6232 (m-30) REVERT: B 1105 THR cc_start: 0.7996 (t) cc_final: 0.7657 (p) REVERT: C 31 SER cc_start: 0.6110 (OUTLIER) cc_final: 0.5280 (p) REVERT: C 535 LYS cc_start: 0.7223 (tmtt) cc_final: 0.6958 (tmtt) REVERT: C 644 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.5081 (mt0) REVERT: C 761 THR cc_start: 0.8425 (m) cc_final: 0.8147 (t) REVERT: C 773 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6076 (mm-30) REVERT: C 854 LYS cc_start: 0.6517 (mtpt) cc_final: 0.6158 (mtpt) REVERT: C 963 VAL cc_start: 0.7866 (t) cc_final: 0.7241 (p) REVERT: C 994 ASP cc_start: 0.6357 (m-30) cc_final: 0.6005 (m-30) REVERT: C 1023 ASN cc_start: 0.7532 (m-40) cc_final: 0.7330 (m110) REVERT: C 1029 MET cc_start: 0.7724 (tpp) cc_final: 0.7133 (tpp) REVERT: C 1048 HIS cc_start: 0.7238 (t70) cc_final: 0.7005 (t70) REVERT: C 1101 HIS cc_start: 0.6544 (OUTLIER) cc_final: 0.6306 (m-70) outliers start: 53 outliers final: 37 residues processed: 457 average time/residue: 0.1664 time to fit residues: 119.9002 Evaluate side-chains 434 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 393 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 216 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 102 optimal weight: 0.0670 chunk 159 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 227 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN B 394 ASN B1134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.224532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.177440 restraints weight = 39662.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178883 restraints weight = 21938.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.181576 restraints weight = 14964.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.182589 restraints weight = 10692.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.182474 restraints weight = 9735.870| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25991 Z= 0.126 Angle : 0.527 9.824 35374 Z= 0.274 Chirality : 0.044 0.195 3981 Planarity : 0.004 0.058 4581 Dihedral : 4.205 24.331 3468 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.91 % Allowed : 9.75 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3201 helix: 0.97 (0.19), residues: 717 sheet: 0.06 (0.18), residues: 678 loop : -1.00 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 328 TYR 0.015 0.001 TYR C1138 PHE 0.020 0.001 PHE A 759 TRP 0.011 0.001 TRP B 64 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00279 (25956) covalent geometry : angle 0.52143 (35304) SS BOND : bond 0.00387 ( 35) SS BOND : angle 1.77674 ( 70) hydrogen bonds : bond 0.03722 ( 944) hydrogen bonds : angle 5.28095 ( 2631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 400 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.6439 (mt) cc_final: 0.6120 (mt) REVERT: A 304 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7599 (mmmm) REVERT: A 417 ASN cc_start: 0.6883 (m-40) cc_final: 0.6457 (t0) REVERT: A 534 VAL cc_start: 0.8044 (t) cc_final: 0.7794 (m) REVERT: A 615 VAL cc_start: 0.6223 (p) cc_final: 0.5072 (t) REVERT: A 699 LEU cc_start: 0.7979 (mt) cc_final: 0.7684 (mp) REVERT: A 704 SER cc_start: 0.8512 (t) cc_final: 0.8038 (p) REVERT: A 737 ASP cc_start: 0.6827 (t70) cc_final: 0.6265 (t70) REVERT: A 775 ASP cc_start: 0.7922 (m-30) cc_final: 0.7048 (t70) REVERT: A 965 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7524 (mm-40) REVERT: A 994 ASP cc_start: 0.7189 (m-30) cc_final: 0.6974 (m-30) REVERT: A 1005 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7409 (tp-100) REVERT: A 1017 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: A 1028 LYS cc_start: 0.7890 (mttt) cc_final: 0.7454 (ttmm) REVERT: A 1029 MET cc_start: 0.7697 (tpp) cc_final: 0.7383 (tpp) REVERT: A 1139 ASP cc_start: 0.7546 (t0) cc_final: 0.7177 (t0) REVERT: B 51 THR cc_start: 0.7796 (t) cc_final: 0.7541 (p) REVERT: B 195 LYS cc_start: 0.6700 (pttt) cc_final: 0.5800 (ttpt) REVERT: B 201 PHE cc_start: 0.6555 (m-10) cc_final: 0.6131 (m-10) REVERT: B 302 THR cc_start: 0.7723 (m) cc_final: 0.7470 (t) REVERT: B 776 LYS cc_start: 0.8290 (mttt) cc_final: 0.8030 (ttmt) REVERT: B 822 LEU cc_start: 0.7763 (mp) cc_final: 0.7510 (mm) REVERT: B 933 LYS cc_start: 0.7813 (mttt) cc_final: 0.7514 (ttmm) REVERT: B 1105 THR cc_start: 0.7956 (t) cc_final: 0.7644 (p) REVERT: C 31 SER cc_start: 0.5982 (OUTLIER) cc_final: 0.5296 (p) REVERT: C 59 PHE cc_start: 0.7184 (m-80) cc_final: 0.6728 (m-80) REVERT: C 644 GLN cc_start: 0.5954 (OUTLIER) cc_final: 0.5697 (mm-40) REVERT: C 773 GLU cc_start: 0.6333 (mm-30) cc_final: 0.5976 (mm-30) REVERT: C 854 LYS cc_start: 0.6555 (mtpt) cc_final: 0.6167 (mtpt) REVERT: C 868 GLU cc_start: 0.7879 (tp30) cc_final: 0.7569 (tp30) REVERT: C 902 MET cc_start: 0.7240 (mmm) cc_final: 0.7028 (mmt) REVERT: C 912 THR cc_start: 0.6253 (m) cc_final: 0.5344 (p) REVERT: C 963 VAL cc_start: 0.7741 (t) cc_final: 0.6991 (p) REVERT: C 994 ASP cc_start: 0.6390 (m-30) cc_final: 0.6045 (m-30) REVERT: C 1023 ASN cc_start: 0.7468 (m-40) cc_final: 0.7255 (m110) REVERT: C 1029 MET cc_start: 0.7601 (tpp) cc_final: 0.7002 (tpp) REVERT: C 1101 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.6303 (m-70) outliers start: 54 outliers final: 36 residues processed: 432 average time/residue: 0.1834 time to fit residues: 123.8877 Evaluate side-chains 429 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 389 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 312 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 289 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 292 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 657 ASN A 764 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 949 GLN B 957 GLN B1005 GLN B1011 GLN B1108 ASN B1134 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.219669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169070 restraints weight = 38553.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173527 restraints weight = 19675.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.176509 restraints weight = 11729.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.177454 restraints weight = 8446.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177905 restraints weight = 7408.512| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 25991 Z= 0.230 Angle : 0.630 10.920 35374 Z= 0.331 Chirality : 0.047 0.194 3981 Planarity : 0.005 0.054 4581 Dihedral : 4.687 25.334 3468 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.12 % Allowed : 10.52 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.14), residues: 3201 helix: 0.76 (0.19), residues: 708 sheet: -0.03 (0.18), residues: 686 loop : -1.14 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.026 0.002 TYR C 789 PHE 0.027 0.002 PHE A1121 TRP 0.010 0.001 TRP A 436 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00518 (25956) covalent geometry : angle 0.62108 (35304) SS BOND : bond 0.00655 ( 35) SS BOND : angle 2.40493 ( 70) hydrogen bonds : bond 0.04367 ( 944) hydrogen bonds : angle 5.57071 ( 2631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 410 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.6349 (mt) cc_final: 0.6037 (mt) REVERT: A 304 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7680 (mmmm) REVERT: A 699 LEU cc_start: 0.8098 (mt) cc_final: 0.7849 (mp) REVERT: A 702 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6433 (tm-30) REVERT: A 704 SER cc_start: 0.8591 (t) cc_final: 0.8188 (p) REVERT: A 737 ASP cc_start: 0.6877 (t70) cc_final: 0.6323 (t70) REVERT: A 775 ASP cc_start: 0.8017 (m-30) cc_final: 0.7083 (t0) REVERT: A 965 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7614 (mm-40) REVERT: A 1005 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7365 (tp-100) REVERT: A 1028 LYS cc_start: 0.7861 (mttt) cc_final: 0.7451 (ttmm) REVERT: A 1041 ASP cc_start: 0.7607 (t0) cc_final: 0.7354 (t0) REVERT: A 1139 ASP cc_start: 0.7621 (t0) cc_final: 0.7304 (t0) REVERT: B 51 THR cc_start: 0.7850 (t) cc_final: 0.7571 (p) REVERT: B 195 LYS cc_start: 0.6877 (pttt) cc_final: 0.5784 (ttpt) REVERT: B 302 THR cc_start: 0.7767 (m) cc_final: 0.7517 (t) REVERT: B 692 ILE cc_start: 0.6798 (mt) cc_final: 0.6200 (mm) REVERT: B 776 LYS cc_start: 0.8282 (mttt) cc_final: 0.8046 (ttmt) REVERT: B 822 LEU cc_start: 0.7921 (mp) cc_final: 0.7689 (mm) REVERT: B 933 LYS cc_start: 0.7889 (mttt) cc_final: 0.7582 (ttmm) REVERT: B 1068 VAL cc_start: 0.6388 (t) cc_final: 0.5500 (p) REVERT: C 31 SER cc_start: 0.6554 (OUTLIER) cc_final: 0.6185 (m) REVERT: C 317 ASN cc_start: 0.6537 (m-40) cc_final: 0.6127 (m-40) REVERT: C 644 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5588 (mt0) REVERT: C 741 TYR cc_start: 0.7555 (t80) cc_final: 0.6973 (t80) REVERT: C 773 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6110 (mm-30) REVERT: C 854 LYS cc_start: 0.6588 (mtpt) cc_final: 0.6243 (mtpt) REVERT: C 912 THR cc_start: 0.6435 (m) cc_final: 0.5575 (p) REVERT: C 963 VAL cc_start: 0.7837 (t) cc_final: 0.7273 (p) REVERT: C 994 ASP cc_start: 0.6522 (m-30) cc_final: 0.6271 (m-30) REVERT: C 1014 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.7227 (ttp-110) REVERT: C 1023 ASN cc_start: 0.7509 (m-40) cc_final: 0.7228 (m110) REVERT: C 1029 MET cc_start: 0.7657 (tpp) cc_final: 0.7051 (tpp) REVERT: C 1101 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6284 (m-70) outliers start: 60 outliers final: 47 residues processed: 442 average time/residue: 0.1802 time to fit residues: 125.1444 Evaluate side-chains 439 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 389 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 95 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 162 optimal weight: 0.0470 chunk 10 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 245 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1134 ASN C 762 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.221924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177533 restraints weight = 39583.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.177251 restraints weight = 25486.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.178448 restraints weight = 17721.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179167 restraints weight = 14426.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.179672 restraints weight = 12876.937| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25991 Z= 0.134 Angle : 0.556 10.733 35374 Z= 0.288 Chirality : 0.044 0.180 3981 Planarity : 0.004 0.055 4581 Dihedral : 4.373 22.751 3468 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.05 % Allowed : 11.23 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3201 helix: 0.97 (0.19), residues: 709 sheet: -0.05 (0.19), residues: 681 loop : -1.06 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.019 0.001 TYR C 170 PHE 0.020 0.001 PHE B 275 TRP 0.011 0.001 TRP B 64 HIS 0.012 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00299 (25956) covalent geometry : angle 0.54983 (35304) SS BOND : bond 0.00464 ( 35) SS BOND : angle 2.00128 ( 70) hydrogen bonds : bond 0.03789 ( 944) hydrogen bonds : angle 5.30339 ( 2631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 396 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ILE cc_start: 0.6210 (mt) cc_final: 0.5866 (mt) REVERT: A 304 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7622 (mmmm) REVERT: A 699 LEU cc_start: 0.7978 (mt) cc_final: 0.7722 (mp) REVERT: A 701 VAL cc_start: 0.8634 (t) cc_final: 0.8350 (p) REVERT: A 702 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6518 (tm-30) REVERT: A 704 SER cc_start: 0.8512 (t) cc_final: 0.8087 (p) REVERT: A 737 ASP cc_start: 0.6796 (t70) cc_final: 0.6142 (t70) REVERT: A 965 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7595 (mm-40) REVERT: A 975 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7697 (t) REVERT: A 1005 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7463 (tp-100) REVERT: A 1017 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 1028 LYS cc_start: 0.7894 (mttt) cc_final: 0.7572 (ttmm) REVERT: A 1029 MET cc_start: 0.7685 (tpp) cc_final: 0.7388 (tpp) REVERT: A 1139 ASP cc_start: 0.7604 (t0) cc_final: 0.7269 (t0) REVERT: B 51 THR cc_start: 0.7816 (t) cc_final: 0.7519 (p) REVERT: B 52 GLN cc_start: 0.7946 (tp-100) cc_final: 0.7739 (tp40) REVERT: B 195 LYS cc_start: 0.6813 (pttt) cc_final: 0.5876 (ttpt) REVERT: B 302 THR cc_start: 0.7773 (m) cc_final: 0.7506 (t) REVERT: B 592 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6068 (p90) REVERT: B 692 ILE cc_start: 0.6783 (mt) cc_final: 0.6130 (mm) REVERT: B 776 LYS cc_start: 0.8291 (mttt) cc_final: 0.8047 (ttmt) REVERT: B 822 LEU cc_start: 0.7813 (mp) cc_final: 0.7557 (mm) REVERT: B 933 LYS cc_start: 0.7826 (mttt) cc_final: 0.7521 (ttmm) REVERT: B 1045 LYS cc_start: 0.7437 (tptt) cc_final: 0.7228 (tptt) REVERT: B 1091 ARG cc_start: 0.6900 (ptm160) cc_final: 0.6568 (ptp-110) REVERT: C 31 SER cc_start: 0.6178 (OUTLIER) cc_final: 0.5574 (p) REVERT: C 317 ASN cc_start: 0.6384 (m-40) cc_final: 0.5954 (m-40) REVERT: C 583 GLU cc_start: 0.5507 (tt0) cc_final: 0.5279 (tt0) REVERT: C 741 TYR cc_start: 0.7468 (t80) cc_final: 0.7036 (t80) REVERT: C 773 GLU cc_start: 0.6313 (mm-30) cc_final: 0.6086 (mm-30) REVERT: C 776 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7665 (tmtt) REVERT: C 854 LYS cc_start: 0.6460 (mtpt) cc_final: 0.6141 (mtpt) REVERT: C 912 THR cc_start: 0.6322 (m) cc_final: 0.5438 (p) REVERT: C 963 VAL cc_start: 0.7753 (t) cc_final: 0.7204 (p) REVERT: C 974 SER cc_start: 0.8446 (m) cc_final: 0.7891 (p) REVERT: C 980 ILE cc_start: 0.7229 (mm) cc_final: 0.7025 (mp) REVERT: C 994 ASP cc_start: 0.6473 (m-30) cc_final: 0.6138 (m-30) REVERT: C 1023 ASN cc_start: 0.7516 (m-40) cc_final: 0.7238 (m110) REVERT: C 1029 MET cc_start: 0.7626 (tpp) cc_final: 0.7004 (tpp) REVERT: C 1101 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.6237 (m-70) outliers start: 58 outliers final: 40 residues processed: 428 average time/residue: 0.1799 time to fit residues: 120.1930 Evaluate side-chains 430 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 386 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 73 optimal weight: 0.0010 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 657 ASN A 895 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 957 GLN B1134 ASN C 66 HIS C 762 GLN C 895 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.220606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175789 restraints weight = 39478.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.175106 restraints weight = 25123.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.176964 restraints weight = 18990.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.178275 restraints weight = 13851.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.178177 restraints weight = 11678.606| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25991 Z= 0.162 Angle : 0.579 11.656 35374 Z= 0.300 Chirality : 0.045 0.196 3981 Planarity : 0.004 0.053 4581 Dihedral : 4.423 21.406 3468 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.87 % Allowed : 11.51 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3201 helix: 0.92 (0.19), residues: 712 sheet: -0.04 (0.19), residues: 687 loop : -1.08 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1091 TYR 0.019 0.001 TYR A1067 PHE 0.026 0.002 PHE A 643 TRP 0.010 0.001 TRP B 64 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00363 (25956) covalent geometry : angle 0.57323 (35304) SS BOND : bond 0.00496 ( 35) SS BOND : angle 1.94489 ( 70) hydrogen bonds : bond 0.03873 ( 944) hydrogen bonds : angle 5.36162 ( 2631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 400 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5414 (m-10) cc_final: 0.5154 (m-10) REVERT: A 285 ILE cc_start: 0.6273 (mt) cc_final: 0.5934 (mt) REVERT: A 699 LEU cc_start: 0.8012 (mt) cc_final: 0.7734 (mp) REVERT: A 701 VAL cc_start: 0.8682 (t) cc_final: 0.8453 (p) REVERT: A 702 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6537 (tm-30) REVERT: A 704 SER cc_start: 0.8516 (t) cc_final: 0.8113 (p) REVERT: A 737 ASP cc_start: 0.6821 (t70) cc_final: 0.6219 (t70) REVERT: A 965 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7614 (mm-40) REVERT: A 1005 GLN cc_start: 0.7708 (tp-100) cc_final: 0.7313 (tp-100) REVERT: A 1017 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6314 (tm-30) REVERT: A 1028 LYS cc_start: 0.7918 (mttt) cc_final: 0.7400 (mtpp) REVERT: A 1029 MET cc_start: 0.7699 (tpp) cc_final: 0.7403 (tpp) REVERT: A 1139 ASP cc_start: 0.7633 (t0) cc_final: 0.7276 (t0) REVERT: B 51 THR cc_start: 0.7800 (t) cc_final: 0.7527 (p) REVERT: B 195 LYS cc_start: 0.6893 (pttt) cc_final: 0.5907 (ttpt) REVERT: B 302 THR cc_start: 0.7773 (m) cc_final: 0.7523 (t) REVERT: B 592 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6100 (p90) REVERT: B 692 ILE cc_start: 0.6844 (mt) cc_final: 0.6207 (mm) REVERT: B 776 LYS cc_start: 0.8258 (mttt) cc_final: 0.8040 (ttmt) REVERT: B 822 LEU cc_start: 0.7853 (mp) cc_final: 0.7628 (mm) REVERT: B 867 ASP cc_start: 0.6704 (m-30) cc_final: 0.6439 (m-30) REVERT: B 933 LYS cc_start: 0.7840 (mttt) cc_final: 0.7535 (ttmm) REVERT: B 1045 LYS cc_start: 0.7472 (tptt) cc_final: 0.7220 (tptt) REVERT: C 31 SER cc_start: 0.6212 (OUTLIER) cc_final: 0.5799 (m) REVERT: C 129 LYS cc_start: 0.6236 (tppt) cc_final: 0.5750 (tppt) REVERT: C 317 ASN cc_start: 0.6445 (m-40) cc_final: 0.6043 (m-40) REVERT: C 644 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5573 (mt0) REVERT: C 741 TYR cc_start: 0.7455 (t80) cc_final: 0.6967 (t80) REVERT: C 773 GLU cc_start: 0.6328 (mm-30) cc_final: 0.6121 (mm-30) REVERT: C 776 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7726 (tmtt) REVERT: C 854 LYS cc_start: 0.6478 (mtpt) cc_final: 0.6151 (mtpt) REVERT: C 912 THR cc_start: 0.6425 (m) cc_final: 0.5538 (p) REVERT: C 963 VAL cc_start: 0.7787 (t) cc_final: 0.7240 (p) REVERT: C 964 LYS cc_start: 0.7567 (mttt) cc_final: 0.7314 (mmpt) REVERT: C 974 SER cc_start: 0.8408 (m) cc_final: 0.7874 (p) REVERT: C 980 ILE cc_start: 0.7262 (mm) cc_final: 0.7009 (mp) REVERT: C 994 ASP cc_start: 0.6278 (m-30) cc_final: 0.5956 (m-30) REVERT: C 1014 ARG cc_start: 0.7410 (ttp-110) cc_final: 0.7154 (ttp-110) REVERT: C 1023 ASN cc_start: 0.7470 (m-40) cc_final: 0.7213 (m110) REVERT: C 1029 MET cc_start: 0.7610 (tpp) cc_final: 0.6852 (tpp) REVERT: C 1101 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.6209 (m-70) outliers start: 53 outliers final: 43 residues processed: 427 average time/residue: 0.1826 time to fit residues: 121.3417 Evaluate side-chains 433 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 386 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 4 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 311 optimal weight: 0.3980 chunk 312 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN A 901 GLN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1134 ASN C 762 GLN C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.221337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.176509 restraints weight = 39654.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.176824 restraints weight = 25138.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.178434 restraints weight = 16820.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.179503 restraints weight = 13739.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.179272 restraints weight = 11729.938| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25991 Z= 0.138 Angle : 0.570 12.285 35374 Z= 0.295 Chirality : 0.045 0.193 3981 Planarity : 0.004 0.085 4581 Dihedral : 4.368 21.530 3468 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.84 % Allowed : 12.01 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3201 helix: 0.91 (0.19), residues: 718 sheet: -0.03 (0.19), residues: 685 loop : -1.06 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 995 TYR 0.017 0.001 TYR C 170 PHE 0.024 0.001 PHE A 643 TRP 0.016 0.001 TRP C 64 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00311 (25956) covalent geometry : angle 0.56413 (35304) SS BOND : bond 0.00456 ( 35) SS BOND : angle 1.87640 ( 70) hydrogen bonds : bond 0.03715 ( 944) hydrogen bonds : angle 5.29922 ( 2631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 390 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7023 (t80) cc_final: 0.6652 (t80) REVERT: A 106 PHE cc_start: 0.5333 (m-10) cc_final: 0.5074 (m-10) REVERT: A 701 VAL cc_start: 0.8695 (t) cc_final: 0.8471 (p) REVERT: A 702 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 704 SER cc_start: 0.8499 (t) cc_final: 0.8081 (p) REVERT: A 737 ASP cc_start: 0.6754 (t70) cc_final: 0.6134 (t70) REVERT: A 748 GLU cc_start: 0.7529 (mp0) cc_final: 0.6989 (mp0) REVERT: A 825 LYS cc_start: 0.8251 (ptpp) cc_final: 0.8002 (ptmt) REVERT: A 965 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7573 (mm-40) REVERT: A 1005 GLN cc_start: 0.7738 (tp-100) cc_final: 0.7498 (tp-100) REVERT: A 1017 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6377 (tm-30) REVERT: A 1028 LYS cc_start: 0.7901 (mttt) cc_final: 0.7502 (ttmm) REVERT: A 1029 MET cc_start: 0.7705 (tpp) cc_final: 0.7432 (tpp) REVERT: A 1139 ASP cc_start: 0.7638 (t0) cc_final: 0.7288 (t0) REVERT: B 51 THR cc_start: 0.7834 (t) cc_final: 0.7575 (p) REVERT: B 195 LYS cc_start: 0.6897 (pttt) cc_final: 0.5967 (ttpt) REVERT: B 302 THR cc_start: 0.7743 (m) cc_final: 0.7500 (t) REVERT: B 328 ARG cc_start: 0.6366 (ttm-80) cc_final: 0.6056 (ttm-80) REVERT: B 592 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6109 (p90) REVERT: B 692 ILE cc_start: 0.6824 (mt) cc_final: 0.6160 (mm) REVERT: B 740 MET cc_start: 0.6956 (ttt) cc_final: 0.6741 (ttm) REVERT: B 776 LYS cc_start: 0.8272 (mttt) cc_final: 0.8032 (ttmt) REVERT: B 822 LEU cc_start: 0.7815 (mp) cc_final: 0.7595 (mm) REVERT: B 933 LYS cc_start: 0.7830 (mttt) cc_final: 0.7545 (ttmm) REVERT: B 1045 LYS cc_start: 0.7443 (tptt) cc_final: 0.7194 (tptt) REVERT: C 31 SER cc_start: 0.6066 (OUTLIER) cc_final: 0.5667 (m) REVERT: C 44 ARG cc_start: 0.7738 (mtt-85) cc_final: 0.7286 (mtt90) REVERT: C 317 ASN cc_start: 0.6226 (m-40) cc_final: 0.5867 (m-40) REVERT: C 644 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5522 (mt0) REVERT: C 854 LYS cc_start: 0.6457 (mtpt) cc_final: 0.6152 (mtpt) REVERT: C 869 MET cc_start: 0.6715 (ptp) cc_final: 0.6476 (ptp) REVERT: C 912 THR cc_start: 0.6345 (m) cc_final: 0.5475 (p) REVERT: C 964 LYS cc_start: 0.7550 (mttt) cc_final: 0.7232 (mmpt) REVERT: C 974 SER cc_start: 0.8358 (m) cc_final: 0.7985 (p) REVERT: C 980 ILE cc_start: 0.7022 (mm) cc_final: 0.6778 (tp) REVERT: C 994 ASP cc_start: 0.6283 (m-30) cc_final: 0.5992 (m-30) REVERT: C 1029 MET cc_start: 0.7616 (tpp) cc_final: 0.6811 (tpp) REVERT: C 1101 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.6188 (m-70) outliers start: 52 outliers final: 42 residues processed: 415 average time/residue: 0.1712 time to fit residues: 112.2183 Evaluate side-chains 425 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 166 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 212 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 217 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 824 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN C 762 GLN C 895 GLN C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.221426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.176449 restraints weight = 39546.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.176762 restraints weight = 26233.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.180033 restraints weight = 16313.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.180337 restraints weight = 12416.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.180115 restraints weight = 10912.046| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25991 Z= 0.130 Angle : 0.577 12.975 35374 Z= 0.297 Chirality : 0.045 0.221 3981 Planarity : 0.004 0.083 4581 Dihedral : 4.307 21.792 3468 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.55 % Allowed : 12.54 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3201 helix: 0.96 (0.19), residues: 712 sheet: -0.03 (0.19), residues: 670 loop : -1.03 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1091 TYR 0.017 0.001 TYR C 170 PHE 0.024 0.001 PHE A 759 TRP 0.011 0.001 TRP B 64 HIS 0.011 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00293 (25956) covalent geometry : angle 0.57226 (35304) SS BOND : bond 0.00454 ( 35) SS BOND : angle 1.71966 ( 70) hydrogen bonds : bond 0.03640 ( 944) hydrogen bonds : angle 5.29464 ( 2631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 388 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 PHE cc_start: 0.6970 (t80) cc_final: 0.6486 (t80) REVERT: A 106 PHE cc_start: 0.5300 (m-10) cc_final: 0.5055 (m-10) REVERT: A 701 VAL cc_start: 0.8745 (t) cc_final: 0.8499 (p) REVERT: A 702 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 704 SER cc_start: 0.8497 (t) cc_final: 0.8082 (p) REVERT: A 737 ASP cc_start: 0.6779 (t70) cc_final: 0.6171 (t70) REVERT: A 748 GLU cc_start: 0.7501 (mp0) cc_final: 0.7077 (mp0) REVERT: A 825 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7986 (ptmt) REVERT: A 965 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7570 (mm-40) REVERT: A 1005 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7515 (tp-100) REVERT: A 1017 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6407 (tm-30) REVERT: A 1028 LYS cc_start: 0.7868 (mttt) cc_final: 0.7630 (ttmt) REVERT: A 1029 MET cc_start: 0.7666 (tpp) cc_final: 0.7393 (tpp) REVERT: A 1139 ASP cc_start: 0.7634 (t0) cc_final: 0.7275 (t0) REVERT: B 51 THR cc_start: 0.7914 (t) cc_final: 0.7644 (p) REVERT: B 195 LYS cc_start: 0.6905 (pttt) cc_final: 0.5974 (ttpt) REVERT: B 302 THR cc_start: 0.7740 (m) cc_final: 0.7508 (t) REVERT: B 592 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6166 (p90) REVERT: B 692 ILE cc_start: 0.6798 (mt) cc_final: 0.6132 (mm) REVERT: B 740 MET cc_start: 0.7180 (ttt) cc_final: 0.6961 (ttm) REVERT: B 776 LYS cc_start: 0.8270 (mttt) cc_final: 0.8026 (ttmt) REVERT: B 933 LYS cc_start: 0.7817 (mttt) cc_final: 0.7516 (ttmm) REVERT: B 995 ARG cc_start: 0.7593 (tpp80) cc_final: 0.6969 (ttp80) REVERT: B 1031 GLU cc_start: 0.6581 (mp0) cc_final: 0.6367 (mp0) REVERT: B 1045 LYS cc_start: 0.7359 (tptt) cc_final: 0.7120 (tptt) REVERT: C 31 SER cc_start: 0.5985 (OUTLIER) cc_final: 0.5598 (m) REVERT: C 317 ASN cc_start: 0.6192 (m-40) cc_final: 0.5843 (m-40) REVERT: C 644 GLN cc_start: 0.6175 (OUTLIER) cc_final: 0.5455 (mt0) REVERT: C 776 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7721 (tmtt) REVERT: C 825 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7544 (mttt) REVERT: C 854 LYS cc_start: 0.6304 (mtpt) cc_final: 0.6006 (mtpt) REVERT: C 869 MET cc_start: 0.6731 (ptp) cc_final: 0.6493 (ptp) REVERT: C 912 THR cc_start: 0.6348 (m) cc_final: 0.5483 (p) REVERT: C 963 VAL cc_start: 0.7744 (t) cc_final: 0.7270 (p) REVERT: C 964 LYS cc_start: 0.7542 (mttt) cc_final: 0.7296 (mmpt) REVERT: C 974 SER cc_start: 0.8297 (m) cc_final: 0.7971 (p) REVERT: C 980 ILE cc_start: 0.7042 (mm) cc_final: 0.6826 (tp) REVERT: C 1000 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7148 (mtt-85) REVERT: C 1029 MET cc_start: 0.7524 (tpp) cc_final: 0.6827 (tpp) REVERT: C 1101 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.6171 (m-70) outliers start: 44 outliers final: 37 residues processed: 409 average time/residue: 0.1631 time to fit residues: 106.4527 Evaluate side-chains 420 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 704 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 111 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 242 optimal weight: 0.0030 chunk 90 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 128 optimal weight: 0.9990 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 ASN ** C 755 GLN ** 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 = 0.4698 r_free = 0.4698 target = 0.221441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.176831 restraints weight = 39542.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.177017 restraints weight = 25983.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.180003 restraints weight = 16348.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.180310 restraints weight = 12782.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.180114 restraints weight = 11075.697| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 25991 Z= 0.155 Angle : 0.724 59.200 35374 Z= 0.401 Chirality : 0.045 0.419 3981 Planarity : 0.004 0.083 4581 Dihedral : 4.327 28.271 3468 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.59 % Allowed : 12.64 % Favored : 85.77 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3201 helix: 0.95 (0.19), residues: 712 sheet: -0.03 (0.19), residues: 670 loop : -1.03 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.017 0.001 TYR A1067 PHE 0.024 0.001 PHE A 759 TRP 0.011 0.001 TRP C 64 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (25956) covalent geometry : angle 0.70434 (35304) SS BOND : bond 0.01213 ( 35) SS BOND : angle 3.84481 ( 70) hydrogen bonds : bond 0.03642 ( 944) hydrogen bonds : angle 5.29575 ( 2631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6230.30 seconds wall clock time: 107 minutes 24.97 seconds (6444.97 seconds total)