Starting phenix.real_space_refine on Sun Jul 5 16:08:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru5_24697/07_2026/7ru5_24697.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 138 5.16 5 C 18216 2.51 5 N 4734 2.21 5 O 5585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28673 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 8527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8527 Classifications: {'peptide': 1093} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8025 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 11 Chain: "B" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8025 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 11 Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.64, per 1000 atoms: 0.23 Number of scatterers: 28673 At special positions: 0 Unit cell: (146.26, 151.41, 229.69, 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 138 16.00 O 5585 8.00 N 4734 7.00 C 18216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.12 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS A 883 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.06 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS B 705 " 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=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.10 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100D" distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 148 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 801 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6742 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 64 sheets defined 23.7% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.484A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 843 removed outlier: 4.091A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.785A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (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 967 removed outlier: 3.647A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.550A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.536A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.980A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 84 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 84 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.139A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.122A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.423A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.438A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.894A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.936A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.874A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.874A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.773A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.782A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.479A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.807A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.798A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'C' and resid 787 through 789 Processing sheet with id=AC2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.698A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.993A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.565A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.207A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.427A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.541A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.325A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.919A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.919A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.542A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AD4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.763A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.616A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.563A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.380A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.399A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.971A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.951A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.631A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.414A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AE9, first strand: chain 'B' and resid 423 through 424 Processing sheet with id=AF1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.434A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.100A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.795A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.790A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 96 through 100 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AG3, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.810A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'D' and resid 58 through 59 removed outlier: 5.758A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 96 through 100 Processing sheet with id=AG7, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 46 removed outlier: 4.284A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 48 through 49 1231 hydrogen bonds defined for protein. 3363 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: 8.93 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5423 1.32 - 1.46: 10892 1.46 - 1.61: 12804 1.61 - 1.76: 38 1.76 - 1.91: 152 Bond restraints: 29309 Sorted by residual: bond pdb=" CB LEU B 387 " pdb=" CG LEU B 387 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" CB HIS C1048 " pdb=" CG HIS C1048 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" CB LEU A 387 " pdb=" CG LEU A 387 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" CB HIS C1064 " pdb=" CG HIS C1064 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 bond pdb=" NE ARG L 96 " pdb=" CZ ARG L 96 " ideal model delta sigma weight residual 1.326 1.386 -0.060 1.10e-02 8.26e+03 3.02e+01 ... (remaining 29304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.44: 39741 7.44 - 14.88: 113 14.88 - 22.33: 0 22.33 - 29.77: 0 29.77 - 37.21: 1 Bond angle restraints: 39855 Sorted by residual: angle pdb=" C2 NAG B1303 " pdb=" N2 NAG B1303 " pdb=" C7 NAG B1303 " ideal model delta sigma weight residual 124.56 161.77 -37.21 3.00e+00 1.11e-01 1.54e+02 angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 110.82 100.29 10.53 9.70e-01 1.06e+00 1.18e+02 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 122.96 -10.36 1.00e+00 1.00e+00 1.07e+02 angle pdb=" N ARG D 94 " pdb=" CA ARG D 94 " pdb=" C ARG D 94 " ideal model delta sigma weight residual 113.17 125.10 -11.93 1.26e+00 6.30e-01 8.96e+01 angle pdb=" N ARG H 94 " pdb=" CA ARG H 94 " pdb=" C ARG H 94 " ideal model delta sigma weight residual 113.17 124.80 -11.63 1.26e+00 6.30e-01 8.52e+01 ... (remaining 39850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16573 17.96 - 35.92: 394 35.92 - 53.88: 138 53.88 - 71.84: 52 71.84 - 89.80: 24 Dihedral angle restraints: 17181 sinusoidal: 6700 harmonic: 10481 Sorted by residual: dihedral pdb=" CB CYS C 705 " pdb=" SG CYS C 705 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual 93.00 174.27 -81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 164.90 -71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 160.91 -67.91 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 17178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3336 0.107 - 0.214: 992 0.214 - 0.321: 211 0.321 - 0.428: 61 0.428 - 0.535: 23 Chirality restraints: 4623 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4620 not shown) Planarity restraints: 5132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.089 2.00e-02 2.50e+03 9.47e-02 1.12e+02 pdb=" CG ASN A 616 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.148 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.065 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" CG ASN A 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " 0.055 2.00e-02 2.50e+03 5.91e-02 4.37e+01 pdb=" CG ASN B 616 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " -0.093 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " 0.072 2.00e-02 2.50e+03 ... (remaining 5129 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 12127 2.91 - 3.41: 27104 3.41 - 3.91: 50650 3.91 - 4.40: 58477 4.40 - 4.90: 92068 Nonbonded interactions: 240426 Sorted by model distance: nonbonded pdb=" N ASN C 149 " pdb=" N LYS C 150 " model vdw 2.413 2.560 nonbonded pdb=" N ASP A1084 " pdb=" OD1 ASP A1084 " model vdw 2.430 3.120 nonbonded pdb=" N ARG C 44 " pdb=" O ARG C 44 " model vdw 2.440 2.496 nonbonded pdb=" O GLN B 498 " pdb=" ND2 ASN B 501 " model vdw 2.440 3.120 nonbonded pdb=" N ASP A 111 " pdb=" OD1 ASP A 111 " model vdw 2.449 3.120 ... (remaining 240421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1306) selection = (chain 'C' and (resid 14 through 66 or resid 79 through 143 or resid 153 through \ 175 or resid 185 through 260 or resid 263 through 387 or resid 395 through 426 \ or resid 429 through 515 or resid 522 through 637 or resid 641 through 827 or re \ sid 848 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.700 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.800 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 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:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.020 0.128 29399 Z= 1.078 Angle : 1.829 37.211 40075 Z= 1.223 Chirality : 0.115 0.535 4623 Planarity : 0.009 0.047 5102 Dihedral : 10.343 89.802 10289 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.13), residues: 3545 helix: 0.68 (0.17), residues: 704 sheet: 0.90 (0.18), residues: 764 loop : 0.04 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 457 TYR 0.083 0.010 TYR A 489 PHE 0.060 0.007 PHE B 342 TRP 0.069 0.012 TRP H 47 HIS 0.012 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.02021 / 1.07 (29309) covalent geometry : angle 1.81837 / 1.22 (39855) SS BOND : bond 0.01840 / 0.97 ( 50) SS BOND : angle 3.01659 / 2.09 ( 100) hydrogen bonds : bond 0.16301 / 10.73 ( 1216) hydrogen bonds : angle 8.37027 / 5.77 ( 3363) link_BETA1-4 : bond 0.07037 / 3.83 ( 10) link_BETA1-4 : angle 5.06578 / 3.40 ( 30) link_NAG-ASN : bond 0.08176 / 5.30 ( 30) link_NAG-ASN : angle 2.54766 / 1.81 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.9210 (mtp) cc_final: 0.8941 (mtt) REVERT: C 780 GLU cc_start: 0.8537 (tp30) cc_final: 0.8149 (tp30) REVERT: C 1121 PHE cc_start: 0.6782 (t80) cc_final: 0.6581 (t80) REVERT: A 140 PHE cc_start: 0.6808 (m-80) cc_final: 0.6534 (m-80) REVERT: A 153 MET cc_start: 0.7288 (ttp) cc_final: 0.5117 (ptt) REVERT: B 731 MET cc_start: 0.8820 (ttp) cc_final: 0.8614 (ttm) REVERT: H 36 TRP cc_start: 0.6112 (m100) cc_final: 0.4866 (m100) REVERT: H 47 TRP cc_start: 0.4745 (t60) cc_final: 0.3721 (t60) REVERT: H 63 PHE cc_start: 0.6224 (m-80) cc_final: 0.5628 (m-80) REVERT: H 100 TYR cc_start: 0.4997 (m-80) cc_final: 0.4686 (m-80) REVERT: H 100 PHE cc_start: 0.6485 (m-10) cc_final: 0.5639 (m-80) REVERT: D 82 LEU cc_start: 0.3850 (mt) cc_final: 0.3170 (mp) REVERT: E 48 ILE cc_start: 0.9026 (mt) cc_final: 0.8503 (mp) REVERT: E 98 PHE cc_start: 0.0354 (m-80) cc_final: -0.0029 (m-80) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.2207 time to fit residues: 51.3073 Evaluate side-chains 91 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 414 GLN C 955 ASN A 321 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 856 ASN B 901 GLN H 1 GLN H 64 GLN L 37 GLN D 1 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.075071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.048137 restraints weight = 188442.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.049460 restraints weight = 91334.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.049533 restraints weight = 49959.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049673 restraints weight = 42066.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.049738 restraints weight = 41060.739| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29399 Z= 0.172 Angle : 0.681 9.690 40075 Z= 0.369 Chirality : 0.046 0.338 4623 Planarity : 0.005 0.068 5102 Dihedral : 5.353 25.896 3866 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.67 % Allowed : 2.19 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.62 (0.13), residues: 3545 helix: 2.31 (0.19), residues: 710 sheet: 0.49 (0.17), residues: 826 loop : -0.29 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1107 TYR 0.028 0.002 TYR D 98 PHE 0.030 0.002 PHE L 62 TRP 0.027 0.002 TRP C 258 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (29309) covalent geometry : angle 0.66581 / 0.37 (39855) SS BOND : bond 0.00344 / 0.23 ( 50) SS BOND : angle 1.08502 / 0.73 ( 100) hydrogen bonds : bond 0.05727 / 3.74 ( 1216) hydrogen bonds : angle 6.67049 / 4.58 ( 3363) link_BETA1-4 : bond 0.00587 / 0.27 ( 10) link_BETA1-4 : angle 2.49678 / 1.55 ( 30) link_NAG-ASN : bond 0.00575 / 0.34 ( 30) link_NAG-ASN : angle 2.61425 / 1.94 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.8871 (mtp) cc_final: 0.8554 (mtt) REVERT: A 140 PHE cc_start: 0.6374 (m-80) cc_final: 0.6110 (m-80) REVERT: A 153 MET cc_start: 0.7503 (ttp) cc_final: 0.6692 (tpp) REVERT: H 48 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.4046 (mpp) REVERT: E 98 PHE cc_start: 0.5628 (m-80) cc_final: 0.5355 (m-10) outliers start: 21 outliers final: 10 residues processed: 126 average time/residue: 0.1855 time to fit residues: 39.5849 Evaluate side-chains 94 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 178 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 519 HIS A 655 HIS A 914 ASN B 207 HIS B 655 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.048296 restraints weight = 188720.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.047550 restraints weight = 86989.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.048045 restraints weight = 53945.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.048338 restraints weight = 40330.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048624 restraints weight = 34853.779| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29399 Z= 0.197 Angle : 0.636 9.609 40075 Z= 0.336 Chirality : 0.045 0.321 4623 Planarity : 0.004 0.062 5102 Dihedral : 5.014 22.715 3866 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 0.73 % Allowed : 3.37 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.41 (0.14), residues: 3545 helix: 2.61 (0.19), residues: 710 sheet: 0.11 (0.17), residues: 887 loop : -0.52 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 38 TYR 0.022 0.002 TYR A1067 PHE 0.030 0.002 PHE H 100F TRP 0.021 0.002 TRP C 258 HIS 0.007 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (29309) covalent geometry : angle 0.62503 / 0.33 (39855) SS BOND : bond 0.00306 / 0.21 ( 50) SS BOND : angle 0.97499 / 0.64 ( 100) hydrogen bonds : bond 0.04977 / 3.27 ( 1216) hydrogen bonds : angle 6.16190 / 4.19 ( 3363) link_BETA1-4 : bond 0.00421 / 0.20 ( 10) link_BETA1-4 : angle 1.63132 / 1.03 ( 30) link_NAG-ASN : bond 0.00526 / 0.30 ( 30) link_NAG-ASN : angle 2.22833 / 1.67 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.183 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: C 177 MET cc_start: 0.4971 (tmm) cc_final: 0.4618 (tmm) REVERT: A 153 MET cc_start: 0.7673 (ttp) cc_final: 0.6689 (tpp) REVERT: H 100 TYR cc_start: 0.5105 (m-80) cc_final: 0.4735 (m-80) REVERT: H 100 TRP cc_start: 0.5073 (m100) cc_final: 0.3494 (m100) REVERT: D 98 TYR cc_start: 0.8283 (m-80) cc_final: 0.7962 (m-80) REVERT: E 98 PHE cc_start: 0.4491 (m-80) cc_final: 0.3947 (m-10) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 0.1793 time to fit residues: 33.9324 Evaluate side-chains 98 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 242 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 170 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 316 optimal weight: 30.0000 chunk 140 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 655 HIS C 913 GLN C 955 ASN B 487 ASN H 64 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 64 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.071184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.047328 restraints weight = 186848.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.048514 restraints weight = 91008.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047750 restraints weight = 49664.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.048072 restraints weight = 43114.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048075 restraints weight = 40593.007| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 29399 Z= 0.266 Angle : 0.677 10.102 40075 Z= 0.349 Chirality : 0.046 0.313 4623 Planarity : 0.005 0.043 5102 Dihedral : 5.105 23.163 3866 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer: Outliers : 0.83 % Allowed : 3.94 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.15 (0.14), residues: 3545 helix: 2.56 (0.19), residues: 700 sheet: -0.24 (0.16), residues: 914 loop : -0.64 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1107 TYR 0.024 0.002 TYR H 91 PHE 0.038 0.002 PHE B 906 TRP 0.022 0.002 TRP E 35 HIS 0.008 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 (29309) covalent geometry : angle 0.66566 / 0.35 (39855) SS BOND : bond 0.00419 / 0.28 ( 50) SS BOND : angle 0.99359 / 0.68 ( 100) hydrogen bonds : bond 0.04944 / 3.24 ( 1216) hydrogen bonds : angle 6.18804 / 4.22 ( 3363) link_BETA1-4 : bond 0.00457 / 0.23 ( 10) link_BETA1-4 : angle 1.72045 / 1.13 ( 30) link_NAG-ASN : bond 0.00596 / 0.40 ( 30) link_NAG-ASN : angle 2.38881 / 1.81 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.100 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: C 740 MET cc_start: 0.9109 (mtp) cc_final: 0.8689 (mtp) REVERT: A 153 MET cc_start: 0.7886 (ttp) cc_final: 0.7384 (tpp) REVERT: E 35 TRP cc_start: 0.4348 (OUTLIER) cc_final: 0.3098 (m-90) REVERT: E 98 PHE cc_start: 0.3714 (m-80) cc_final: 0.3417 (m-80) outliers start: 26 outliers final: 16 residues processed: 105 average time/residue: 0.1768 time to fit residues: 32.3431 Evaluate side-chains 99 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 72 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 246 optimal weight: 0.0980 chunk 164 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 281 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 356 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 955 ASN B 487 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.072137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.048343 restraints weight = 187484.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.049284 restraints weight = 89359.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.048686 restraints weight = 63214.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.048842 restraints weight = 41595.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.048990 restraints weight = 39346.999| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29399 Z= 0.115 Angle : 0.537 8.933 40075 Z= 0.281 Chirality : 0.044 0.316 4623 Planarity : 0.004 0.043 5102 Dihedral : 4.714 22.097 3866 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.46 % Rotamer: Outliers : 0.54 % Allowed : 4.99 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.33 (0.14), residues: 3545 helix: 2.96 (0.19), residues: 706 sheet: -0.25 (0.16), residues: 926 loop : -0.58 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 96 TYR 0.024 0.001 TYR C 380 PHE 0.033 0.001 PHE H 63 TRP 0.017 0.001 TRP H 36 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (29309) covalent geometry : angle 0.52636 / 0.28 (39855) SS BOND : bond 0.00224 / 0.15 ( 50) SS BOND : angle 0.79426 / 0.55 ( 100) hydrogen bonds : bond 0.04248 / 2.79 ( 1216) hydrogen bonds : angle 5.76081 / 3.92 ( 3363) link_BETA1-4 : bond 0.00408 / 0.21 ( 10) link_BETA1-4 : angle 1.35238 / 0.91 ( 30) link_NAG-ASN : bond 0.00444 / 0.23 ( 30) link_NAG-ASN : angle 2.10813 / 1.58 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4567 (tmm) cc_final: 0.4302 (tmm) REVERT: C 740 MET cc_start: 0.8950 (mtp) cc_final: 0.8562 (mtp) REVERT: C 805 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8832 (tp) REVERT: A 153 MET cc_start: 0.7799 (ttp) cc_final: 0.7196 (tpp) REVERT: H 94 ARG cc_start: 0.3436 (OUTLIER) cc_final: 0.2995 (ttp80) REVERT: D 58 ASN cc_start: 0.0049 (OUTLIER) cc_final: -0.0296 (t0) REVERT: D 98 TYR cc_start: 0.8343 (m-80) cc_final: 0.8042 (m-80) REVERT: E 98 PHE cc_start: 0.3911 (m-80) cc_final: 0.3164 (m-10) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.1781 time to fit residues: 32.2596 Evaluate side-chains 96 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 89 optimal weight: 4.9990 chunk 329 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 53 optimal weight: 0.0370 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 6 GLN D 58 ASN ** E 6 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 = 0.3900 r_free = 0.3900 target = 0.072114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.046143 restraints weight = 187750.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.045610 restraints weight = 90298.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.046121 restraints weight = 56377.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046480 restraints weight = 44704.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.046501 restraints weight = 38383.518| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29399 Z= 0.118 Angle : 0.533 8.453 40075 Z= 0.277 Chirality : 0.043 0.306 4623 Planarity : 0.004 0.044 5102 Dihedral : 4.606 21.967 3866 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 0.64 % Allowed : 5.24 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.35 (0.14), residues: 3545 helix: 3.06 (0.19), residues: 708 sheet: -0.25 (0.17), residues: 872 loop : -0.59 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 96 TYR 0.040 0.001 TYR L 36 PHE 0.029 0.001 PHE D 96 TRP 0.018 0.001 TRP E 35 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (29309) covalent geometry : angle 0.52261 / 0.28 (39855) SS BOND : bond 0.00245 / 0.15 ( 50) SS BOND : angle 0.81530 / 0.53 ( 100) hydrogen bonds : bond 0.04091 / 2.69 ( 1216) hydrogen bonds : angle 5.64743 / 3.85 ( 3363) link_BETA1-4 : bond 0.00309 / 0.15 ( 10) link_BETA1-4 : angle 1.30762 / 0.87 ( 30) link_NAG-ASN : bond 0.00380 / 0.19 ( 30) link_NAG-ASN : angle 2.05398 / 1.54 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.116 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: C 177 MET cc_start: 0.4707 (tmm) cc_final: 0.4352 (tmm) REVERT: C 740 MET cc_start: 0.8932 (mtp) cc_final: 0.8514 (mtp) REVERT: A 153 MET cc_start: 0.7830 (ttp) cc_final: 0.6897 (tpp) REVERT: H 36 TRP cc_start: 0.6484 (m100) cc_final: 0.5520 (m100) REVERT: D 80 MET cc_start: 0.0536 (tpt) cc_final: 0.0285 (tpt) REVERT: E 98 PHE cc_start: 0.5084 (m-80) cc_final: 0.4638 (m-80) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.1933 time to fit residues: 33.3821 Evaluate side-chains 100 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 270 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 138 optimal weight: 30.0000 chunk 315 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 344 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A1088 HIS B1119 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.070905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045713 restraints weight = 188169.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045054 restraints weight = 89226.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.045529 restraints weight = 57164.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.045856 restraints weight = 44894.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046001 restraints weight = 38983.482| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 29399 Z= 0.258 Angle : 0.638 9.513 40075 Z= 0.326 Chirality : 0.045 0.294 4623 Planarity : 0.004 0.047 5102 Dihedral : 4.789 21.907 3866 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.79 % Allowed : 5.43 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.11 (0.14), residues: 3545 helix: 2.82 (0.19), residues: 705 sheet: -0.40 (0.17), residues: 901 loop : -0.73 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 403 TYR 0.022 0.002 TYR B1067 PHE 0.029 0.002 PHE D 96 TRP 0.019 0.002 TRP E 35 HIS 0.008 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (29309) covalent geometry : angle 0.62794 / 0.32 (39855) SS BOND : bond 0.00299 / 0.20 ( 50) SS BOND : angle 0.94241 / 0.63 ( 100) hydrogen bonds : bond 0.04521 / 2.96 ( 1216) hydrogen bonds : angle 5.88767 / 3.99 ( 3363) link_BETA1-4 : bond 0.00366 / 0.18 ( 10) link_BETA1-4 : angle 1.43433 / 0.96 ( 30) link_NAG-ASN : bond 0.00493 / 0.33 ( 30) link_NAG-ASN : angle 2.18749 / 1.65 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.130 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: C 740 MET cc_start: 0.8902 (mtp) cc_final: 0.8462 (mtp) REVERT: A 153 MET cc_start: 0.7575 (ttp) cc_final: 0.6682 (tpp) REVERT: A 740 MET cc_start: 0.9022 (mmm) cc_final: 0.8736 (tpp) REVERT: D 98 TYR cc_start: 0.7437 (m-80) cc_final: 0.7232 (m-80) REVERT: E 35 TRP cc_start: 0.2218 (m-10) cc_final: 0.1782 (m-90) REVERT: E 98 PHE cc_start: 0.5046 (m-80) cc_final: 0.4230 (m-10) outliers start: 25 outliers final: 16 residues processed: 106 average time/residue: 0.1778 time to fit residues: 32.5283 Evaluate side-chains 102 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 340 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.071768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.045320 restraints weight = 188608.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.045781 restraints weight = 92632.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.045642 restraints weight = 59265.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.045955 restraints weight = 45899.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.046127 restraints weight = 40575.587| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29399 Z= 0.118 Angle : 0.534 9.406 40075 Z= 0.277 Chirality : 0.043 0.291 4623 Planarity : 0.004 0.044 5102 Dihedral : 4.566 21.107 3866 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 0.54 % Allowed : 5.81 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.27 (0.14), residues: 3545 helix: 3.06 (0.19), residues: 706 sheet: -0.33 (0.17), residues: 868 loop : -0.66 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.019 0.001 TYR A1067 PHE 0.029 0.001 PHE H 100F TRP 0.049 0.002 TRP H 36 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (29309) covalent geometry : angle 0.52236 / 0.27 (39855) SS BOND : bond 0.00283 / 0.18 ( 50) SS BOND : angle 1.22148 / 0.76 ( 100) hydrogen bonds : bond 0.04059 / 2.67 ( 1216) hydrogen bonds : angle 5.62798 / 3.82 ( 3363) link_BETA1-4 : bond 0.00402 / 0.20 ( 10) link_BETA1-4 : angle 1.27356 / 0.86 ( 30) link_NAG-ASN : bond 0.00400 / 0.21 ( 30) link_NAG-ASN : angle 1.99689 / 1.49 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4469 (tmm) cc_final: 0.4204 (tmm) REVERT: C 740 MET cc_start: 0.9005 (mtp) cc_final: 0.8540 (mtp) REVERT: C 805 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8873 (tp) REVERT: A 153 MET cc_start: 0.7783 (ttp) cc_final: 0.6873 (tpp) REVERT: A 740 MET cc_start: 0.8991 (mmm) cc_final: 0.8720 (tpp) REVERT: H 20 VAL cc_start: -0.0987 (p) cc_final: -0.1254 (p) REVERT: E 98 PHE cc_start: 0.5096 (m-80) cc_final: 0.4628 (m-10) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 0.1714 time to fit residues: 30.5295 Evaluate side-chains 96 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 30 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 353 optimal weight: 50.0000 chunk 272 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 300 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.071002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044433 restraints weight = 189320.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.045795 restraints weight = 96223.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.045250 restraints weight = 55536.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045760 restraints weight = 51313.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.045482 restraints weight = 46305.357| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29399 Z= 0.214 Angle : 0.606 11.162 40075 Z= 0.309 Chirality : 0.044 0.315 4623 Planarity : 0.004 0.044 5102 Dihedral : 4.707 22.754 3866 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 0.54 % Allowed : 6.29 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.20 (0.14), residues: 3545 helix: 2.89 (0.19), residues: 711 sheet: -0.29 (0.17), residues: 849 loop : -0.71 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.043 0.002 TYR L 36 PHE 0.031 0.002 PHE H 100F TRP 0.042 0.002 TRP H 36 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (29309) covalent geometry : angle 0.59186 / 0.31 (39855) SS BOND : bond 0.00280 / 0.18 ( 50) SS BOND : angle 1.52431 / 0.97 ( 100) hydrogen bonds : bond 0.04279 / 2.80 ( 1216) hydrogen bonds : angle 5.76976 / 3.92 ( 3363) link_BETA1-4 : bond 0.00327 / 0.15 ( 10) link_BETA1-4 : angle 1.37182 / 0.93 ( 30) link_NAG-ASN : bond 0.00418 / 0.26 ( 30) link_NAG-ASN : angle 2.25806 / 1.65 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4432 (tmm) cc_final: 0.4132 (tmm) REVERT: C 740 MET cc_start: 0.8982 (mtp) cc_final: 0.8491 (mtp) REVERT: A 153 MET cc_start: 0.7605 (ttp) cc_final: 0.7190 (tpp) REVERT: A 740 MET cc_start: 0.8993 (mmm) cc_final: 0.8771 (tpp) REVERT: H 91 TYR cc_start: 0.6927 (m-10) cc_final: 0.6456 (m-10) REVERT: L 34 ASN cc_start: 0.3497 (m110) cc_final: 0.3160 (t0) REVERT: E 98 PHE cc_start: 0.5056 (m-80) cc_final: 0.4788 (m-80) outliers start: 17 outliers final: 14 residues processed: 104 average time/residue: 0.1782 time to fit residues: 32.5077 Evaluate side-chains 99 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 30 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 292 optimal weight: 2.9990 chunk 253 optimal weight: 30.0000 chunk 355 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 264 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1088 HIS L 34 ASN ** D 6 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 = 0.3853 r_free = 0.3853 target = 0.070705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3131 r_free = 0.3131 target = 0.042837 restraints weight = 187920.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.043832 restraints weight = 93098.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.044017 restraints weight = 50576.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.043705 restraints weight = 47776.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.043656 restraints weight = 49154.740| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 29399 Z= 0.242 Angle : 0.631 9.929 40075 Z= 0.323 Chirality : 0.045 0.284 4623 Planarity : 0.004 0.045 5102 Dihedral : 4.853 21.549 3866 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 0.54 % Allowed : 6.29 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.02 (0.14), residues: 3545 helix: 2.69 (0.19), residues: 711 sheet: -0.43 (0.18), residues: 835 loop : -0.83 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.037 0.002 TYR L 36 PHE 0.044 0.002 PHE A 486 TRP 0.046 0.002 TRP H 36 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (29309) covalent geometry : angle 0.61825 / 0.32 (39855) SS BOND : bond 0.00303 / 0.20 ( 50) SS BOND : angle 1.34092 / 0.86 ( 100) hydrogen bonds : bond 0.04463 / 2.92 ( 1216) hydrogen bonds : angle 5.91174 / 4.01 ( 3363) link_BETA1-4 : bond 0.00338 / 0.16 ( 10) link_BETA1-4 : angle 1.39619 / 0.96 ( 30) link_NAG-ASN : bond 0.00460 / 0.30 ( 30) link_NAG-ASN : angle 2.33291 / 1.70 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: 0.4380 (tmm) cc_final: 0.4138 (tmm) REVERT: C 697 MET cc_start: 0.8564 (tpp) cc_final: 0.8314 (tpp) REVERT: A 153 MET cc_start: 0.7728 (ttp) cc_final: 0.6838 (tpp) REVERT: A 740 MET cc_start: 0.9007 (mmm) cc_final: 0.8802 (tpp) REVERT: E 98 PHE cc_start: 0.4995 (m-80) cc_final: 0.4711 (m-80) outliers start: 17 outliers final: 15 residues processed: 101 average time/residue: 0.1784 time to fit residues: 31.2369 Evaluate side-chains 97 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 1 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 347 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 272 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 64 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.071629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.045678 restraints weight = 187453.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.046222 restraints weight = 89499.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.046822 restraints weight = 61298.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.046669 restraints weight = 45770.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.046899 restraints weight = 41105.847| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29399 Z= 0.110 Angle : 0.535 8.417 40075 Z= 0.277 Chirality : 0.044 0.281 4623 Planarity : 0.004 0.046 5102 Dihedral : 4.623 23.449 3866 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 0.48 % Allowed : 6.29 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.22 (0.14), residues: 3545 helix: 2.99 (0.19), residues: 707 sheet: -0.25 (0.18), residues: 811 loop : -0.73 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1107 TYR 0.032 0.001 TYR L 36 PHE 0.029 0.001 PHE D 96 TRP 0.051 0.002 TRP H 36 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (29309) covalent geometry : angle 0.52383 / 0.27 (39855) SS BOND : bond 0.00207 / 0.13 ( 50) SS BOND : angle 1.08732 / 0.70 ( 100) hydrogen bonds : bond 0.04003 / 2.64 ( 1216) hydrogen bonds : angle 5.61579 / 3.80 ( 3363) link_BETA1-4 : bond 0.00333 / 0.17 ( 10) link_BETA1-4 : angle 1.26286 / 0.87 ( 30) link_NAG-ASN : bond 0.00396 / 0.20 ( 30) link_NAG-ASN : angle 2.06926 / 1.52 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7781.34 seconds wall clock time: 134 minutes 25.74 seconds (8065.74 seconds total)