Starting phenix.real_space_refine on Sun Sep 13 17:31:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.map" model { file = "/net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zp1_11333/09_2026/6zp1_11333.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 108 5.16 5 C 15708 2.51 5 N 4029 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24705 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "B" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7941 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 49, 'TRANS': 967} Chain breaks: 7 Chain: "D" 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: "E" 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: "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: "H" 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: "L" 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: "R" 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.23, per 1000 atoms: 0.25 Number of scatterers: 24705 At special positions: 0 Unit cell: (133.686, 145.357, 162.333, 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 108 16.00 O 4860 8.00 N 4029 7.00 C 15708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG A1321 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1316 " - " ASN B1074 " " NAG B1321 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1316 " - " ASN C1074 " " NAG C1321 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 997.8 milliseconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 48 sheets defined 24.9% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.555A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.255A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.257A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.498A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.555A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.254A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.256A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.499A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.061A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.556A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.255A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.722A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.740A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.256A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.499A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.744A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.339A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.692A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.773A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.433A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.686A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.339A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.691A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.773A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.687A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.477A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.518A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.338A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.691A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.774A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.687A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.021A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 2898 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6274 1.33 - 1.47: 8002 1.47 - 1.60: 10831 1.60 - 1.74: 6 1.74 - 1.87: 129 Bond restraints: 25242 Sorted by residual: bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.371 0.142 3.90e-02 6.57e+02 1.32e+01 bond pdb=" CG1 ILE C 896 " pdb=" CD1 ILE C 896 " ideal model delta sigma weight residual 1.513 1.371 0.142 3.90e-02 6.57e+02 1.32e+01 bond pdb=" CG1 ILE A 896 " pdb=" CD1 ILE A 896 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " ideal model delta sigma weight residual 1.533 1.591 -0.058 1.90e-02 2.77e+03 9.28e+00 bond pdb=" CG GLU B 990 " pdb=" CD GLU B 990 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.27e+00 ... (remaining 25237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 33665 3.92 - 7.84: 609 7.84 - 11.76: 55 11.76 - 15.68: 0 15.68 - 19.60: 3 Bond angle restraints: 34332 Sorted by residual: angle pdb=" CA GLU C 990 " pdb=" CB GLU C 990 " pdb=" CG GLU C 990 " ideal model delta sigma weight residual 114.10 133.70 -19.60 2.00e+00 2.50e-01 9.60e+01 angle pdb=" CA GLU B 990 " pdb=" CB GLU B 990 " pdb=" CG GLU B 990 " ideal model delta sigma weight residual 114.10 133.67 -19.57 2.00e+00 2.50e-01 9.57e+01 angle pdb=" CA GLU A 990 " pdb=" CB GLU A 990 " pdb=" CG GLU A 990 " ideal model delta sigma weight residual 114.10 133.66 -19.56 2.00e+00 2.50e-01 9.57e+01 angle pdb=" C PHE A 429 " pdb=" CA PHE A 429 " pdb=" CB PHE A 429 " ideal model delta sigma weight residual 109.84 120.10 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C PHE C 429 " pdb=" CA PHE C 429 " pdb=" CB PHE C 429 " ideal model delta sigma weight residual 109.84 120.05 -10.21 1.50e+00 4.44e-01 4.64e+01 ... (remaining 34327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 13580 17.48 - 34.96: 691 34.96 - 52.45: 168 52.45 - 69.93: 57 69.93 - 87.41: 27 Dihedral angle restraints: 14523 sinusoidal: 5652 harmonic: 8871 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.60 -80.60 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.59 -80.59 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 173.54 -80.54 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 14520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3699 0.121 - 0.242: 348 0.242 - 0.363: 15 0.363 - 0.484: 15 0.484 - 0.605: 3 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CG LEU A 277 " pdb=" CB LEU A 277 " pdb=" CD1 LEU A 277 " pdb=" CD2 LEU A 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 9.01e+00 chirality pdb=" CG LEU B 277 " pdb=" CB LEU B 277 " pdb=" CD1 LEU B 277 " pdb=" CD2 LEU B 277 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.99e+00 ... (remaining 4077 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 986 " 0.040 2.00e-02 2.50e+03 7.79e-02 6.07e+01 pdb=" C PRO A 986 " -0.135 2.00e-02 2.50e+03 pdb=" O PRO A 986 " 0.048 2.00e-02 2.50e+03 pdb=" N PRO A 987 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 986 " -0.040 2.00e-02 2.50e+03 7.77e-02 6.04e+01 pdb=" C PRO C 986 " 0.135 2.00e-02 2.50e+03 pdb=" O PRO C 986 " -0.048 2.00e-02 2.50e+03 pdb=" N PRO C 987 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 986 " -0.040 2.00e-02 2.50e+03 7.76e-02 6.02e+01 pdb=" C PRO B 986 " 0.134 2.00e-02 2.50e+03 pdb=" O PRO B 986 " -0.048 2.00e-02 2.50e+03 pdb=" N PRO B 987 " -0.047 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2533 2.74 - 3.28: 24214 3.28 - 3.82: 40020 3.82 - 4.36: 48929 4.36 - 4.90: 83428 Nonbonded interactions: 199124 Sorted by model distance: nonbonded pdb=" OG SER A 813 " pdb=" OE2 GLU A 868 " model vdw 2.197 3.040 nonbonded pdb=" OG SER C 813 " pdb=" OE2 GLU C 868 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE2 GLU B 868 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.205 3.040 ... (remaining 199119 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.120 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.011 0.142 25344 Z= 0.447 Angle : 1.342 19.597 34599 Z= 0.751 Chirality : 0.078 0.605 4080 Planarity : 0.008 0.086 4368 Dihedral : 12.260 87.411 8694 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.60 % Favored : 96.10 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.99 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3003 helix: 0.66 (0.19), residues: 615 sheet: 0.91 (0.19), residues: 654 loop : -0.42 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG B 357 TYR 0.099 0.006 TYR B 495 PHE 0.126 0.006 PHE C 490 TRP 0.025 0.004 TRP B 353 HIS 0.016 0.003 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01051 / 0.45 (25242) covalent geometry : angle 1.28717 / 0.74 (34332) SS BOND : bond 0.01206 / 0.77 ( 39) SS BOND : angle 4.67819 / 3.11 ( 78) hydrogen bonds : bond 0.15466 / 10.10 ( 1005) hydrogen bonds : angle 8.20892 / 5.66 ( 2898) link_BETA1-4 : bond 0.00328 / 0.17 ( 15) link_BETA1-4 : angle 1.14010 / 0.75 ( 45) link_NAG-ASN : bond 0.00953 / 0.66 ( 48) link_NAG-ASN : angle 5.02244 / 3.40 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 248 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9171 (tp) cc_final: 0.8941 (tt) REVERT: A 238 PHE cc_start: 0.7015 (p90) cc_final: 0.6763 (p90) REVERT: A 351 TYR cc_start: 0.8222 (p90) cc_final: 0.7727 (p90) REVERT: A 353 TRP cc_start: 0.8180 (p-90) cc_final: 0.7476 (p-90) REVERT: B 351 TYR cc_start: 0.8108 (p90) cc_final: 0.7659 (p90) REVERT: B 353 TRP cc_start: 0.8309 (p-90) cc_final: 0.7471 (p-90) REVERT: B 378 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7596 (tmtt) REVERT: C 64 TRP cc_start: 0.7984 (t60) cc_final: 0.7630 (t60) REVERT: C 351 TYR cc_start: 0.8119 (p90) cc_final: 0.7671 (p90) REVERT: C 378 LYS cc_start: 0.8162 (tmmt) cc_final: 0.7787 (tmtt) outliers start: 9 outliers final: 3 residues processed: 249 average time/residue: 0.1539 time to fit residues: 63.9285 Evaluate side-chains 191 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 66 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.135217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082302 restraints weight = 49111.414| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.16 r_work: 0.2856 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25344 Z= 0.142 Angle : 0.700 12.653 34599 Z= 0.351 Chirality : 0.049 0.359 4080 Planarity : 0.004 0.059 4368 Dihedral : 5.001 52.227 3267 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 0.56 % Allowed : 4.28 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3003 helix: 1.76 (0.20), residues: 651 sheet: 0.52 (0.19), residues: 666 loop : -0.55 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 357 TYR 0.023 0.002 TYR C 380 PHE 0.029 0.002 PHE B 429 TRP 0.017 0.002 TRP A 104 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (25242) covalent geometry : angle 0.64772 / 0.34 (34332) SS BOND : bond 0.00306 / 0.19 ( 39) SS BOND : angle 1.59077 / 1.04 ( 78) hydrogen bonds : bond 0.04588 / 3.02 ( 1005) hydrogen bonds : angle 6.14255 / 4.24 ( 2898) link_BETA1-4 : bond 0.00352 / 0.20 ( 15) link_BETA1-4 : angle 0.81217 / 0.55 ( 45) link_NAG-ASN : bond 0.00720 / 0.51 ( 48) link_NAG-ASN : angle 4.01991 / 2.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6784 (p90) cc_final: 0.6445 (p90) REVERT: A 351 TYR cc_start: 0.8378 (p90) cc_final: 0.8054 (p90) REVERT: A 400 PHE cc_start: 0.9106 (p90) cc_final: 0.8856 (p90) REVERT: A 429 PHE cc_start: 0.8652 (t80) cc_final: 0.8103 (t80) REVERT: A 574 ASP cc_start: 0.7991 (t0) cc_final: 0.7787 (t0) REVERT: B 104 TRP cc_start: 0.7507 (m-90) cc_final: 0.7204 (m-90) REVERT: B 351 TYR cc_start: 0.8236 (p90) cc_final: 0.7964 (p90) REVERT: B 568 ASP cc_start: 0.8185 (t70) cc_final: 0.7841 (p0) REVERT: B 979 ASP cc_start: 0.8939 (t0) cc_final: 0.8723 (t0) REVERT: C 351 TYR cc_start: 0.8298 (p90) cc_final: 0.7990 (p90) REVERT: C 429 PHE cc_start: 0.8590 (t80) cc_final: 0.8387 (t80) REVERT: C 568 ASP cc_start: 0.8241 (t70) cc_final: 0.8030 (p0) REVERT: C 574 ASP cc_start: 0.8031 (t0) cc_final: 0.7788 (t0) REVERT: C 1138 TYR cc_start: 0.8566 (t80) cc_final: 0.8284 (m-10) outliers start: 15 outliers final: 5 residues processed: 250 average time/residue: 0.1477 time to fit residues: 62.4599 Evaluate side-chains 192 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 14 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 143 optimal weight: 40.0000 chunk 63 optimal weight: 0.3980 chunk 236 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.134572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085361 restraints weight = 48886.640| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.33 r_work: 0.2802 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25344 Z= 0.163 Angle : 0.643 12.386 34599 Z= 0.318 Chirality : 0.048 0.322 4080 Planarity : 0.004 0.049 4368 Dihedral : 4.466 46.221 3261 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Rotamer: Outliers : 1.01 % Allowed : 7.48 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3003 helix: 1.93 (0.21), residues: 642 sheet: 0.41 (0.19), residues: 657 loop : -0.46 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1014 TYR 0.024 0.001 TYR C 495 PHE 0.030 0.002 PHE A 515 TRP 0.020 0.002 TRP A 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25242) covalent geometry : angle 0.59587 / 0.31 (34332) SS BOND : bond 0.00503 / 0.32 ( 39) SS BOND : angle 1.29858 / 0.86 ( 78) hydrogen bonds : bond 0.04208 / 2.79 ( 1005) hydrogen bonds : angle 5.71173 / 3.95 ( 2898) link_BETA1-4 : bond 0.00354 / 0.17 ( 15) link_BETA1-4 : angle 0.88046 / 0.58 ( 45) link_NAG-ASN : bond 0.00704 / 0.50 ( 48) link_NAG-ASN : angle 3.66530 / 2.44 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6986 (p90) cc_final: 0.6703 (p90) REVERT: A 351 TYR cc_start: 0.8372 (p90) cc_final: 0.8101 (p90) REVERT: A 400 PHE cc_start: 0.9079 (p90) cc_final: 0.8695 (p90) REVERT: A 429 PHE cc_start: 0.8596 (t80) cc_final: 0.8120 (t80) REVERT: B 104 TRP cc_start: 0.7574 (m-90) cc_final: 0.7235 (m-90) REVERT: B 351 TYR cc_start: 0.8227 (p90) cc_final: 0.7990 (p90) REVERT: B 436 TRP cc_start: 0.8533 (p90) cc_final: 0.7984 (p90) REVERT: B 568 ASP cc_start: 0.8237 (t70) cc_final: 0.8016 (p0) REVERT: B 979 ASP cc_start: 0.8979 (t0) cc_final: 0.8681 (t0) REVERT: C 351 TYR cc_start: 0.8341 (p90) cc_final: 0.8044 (p90) REVERT: C 429 PHE cc_start: 0.8651 (t80) cc_final: 0.8343 (t80) REVERT: C 495 TYR cc_start: 0.6021 (m-80) cc_final: 0.5682 (m-80) REVERT: C 990 GLU cc_start: 0.8224 (pm20) cc_final: 0.7837 (pm20) outliers start: 27 outliers final: 11 residues processed: 223 average time/residue: 0.1463 time to fit residues: 55.6243 Evaluate side-chains 194 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 127 optimal weight: 4.9990 chunk 300 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 360 ASN A 487 ASN B 487 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.079319 restraints weight = 48780.593| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.99 r_work: 0.2816 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25344 Z= 0.162 Angle : 0.619 12.148 34599 Z= 0.306 Chirality : 0.047 0.320 4080 Planarity : 0.004 0.042 4368 Dihedral : 4.266 26.979 3258 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.24 % Allowed : 8.98 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3003 helix: 1.83 (0.21), residues: 648 sheet: 0.31 (0.18), residues: 663 loop : -0.50 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.019 0.001 TYR C 495 PHE 0.026 0.001 PHE B 429 TRP 0.020 0.002 TRP A 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (25242) covalent geometry : angle 0.57511 / 0.30 (34332) SS BOND : bond 0.00472 / 0.30 ( 39) SS BOND : angle 1.19620 / 0.79 ( 78) hydrogen bonds : bond 0.03966 / 2.64 ( 1005) hydrogen bonds : angle 5.49317 / 3.79 ( 2898) link_BETA1-4 : bond 0.00303 / 0.18 ( 15) link_BETA1-4 : angle 0.81960 / 0.56 ( 45) link_NAG-ASN : bond 0.00686 / 0.48 ( 48) link_NAG-ASN : angle 3.49642 / 2.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7108 (p90) cc_final: 0.6869 (p90) REVERT: A 351 TYR cc_start: 0.8404 (p90) cc_final: 0.8124 (p90) REVERT: A 429 PHE cc_start: 0.8695 (t80) cc_final: 0.8259 (t80) REVERT: B 104 TRP cc_start: 0.7705 (m-90) cc_final: 0.7428 (m-90) REVERT: B 351 TYR cc_start: 0.8242 (p90) cc_final: 0.8009 (p90) REVERT: B 436 TRP cc_start: 0.8537 (p90) cc_final: 0.7987 (p90) REVERT: B 515 PHE cc_start: 0.8303 (m-80) cc_final: 0.7932 (m-80) REVERT: B 568 ASP cc_start: 0.8369 (t70) cc_final: 0.8089 (p0) REVERT: B 979 ASP cc_start: 0.8989 (t0) cc_final: 0.8759 (t0) REVERT: B 990 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: C 351 TYR cc_start: 0.8354 (p90) cc_final: 0.8115 (p90) REVERT: C 429 PHE cc_start: 0.8696 (t80) cc_final: 0.8335 (t80) outliers start: 33 outliers final: 18 residues processed: 222 average time/residue: 0.1460 time to fit residues: 54.8936 Evaluate side-chains 197 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 138 optimal weight: 30.0000 chunk 251 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 241 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 762 GLN B 544 ASN B 901 GLN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 957 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078828 restraints weight = 48730.897| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.03 r_work: 0.2783 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 25344 Z= 0.209 Angle : 0.636 11.940 34599 Z= 0.315 Chirality : 0.047 0.320 4080 Planarity : 0.004 0.051 4368 Dihedral : 4.261 27.544 3258 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.43 % Allowed : 9.43 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3003 helix: 1.90 (0.21), residues: 633 sheet: 0.30 (0.19), residues: 654 loop : -0.56 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.022 0.001 TYR C1138 PHE 0.020 0.001 PHE C 515 TRP 0.022 0.002 TRP A 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (25242) covalent geometry : angle 0.58906 / 0.30 (34332) SS BOND : bond 0.00534 / 0.31 ( 39) SS BOND : angle 2.19049 / 1.40 ( 78) hydrogen bonds : bond 0.04006 / 2.68 ( 1005) hydrogen bonds : angle 5.50395 / 3.80 ( 2898) link_BETA1-4 : bond 0.00358 / 0.21 ( 15) link_BETA1-4 : angle 0.91549 / 0.62 ( 45) link_NAG-ASN : bond 0.00674 / 0.47 ( 48) link_NAG-ASN : angle 3.41103 / 2.26 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7252 (p90) cc_final: 0.6693 (p90) REVERT: A 351 TYR cc_start: 0.8402 (p90) cc_final: 0.8141 (p90) REVERT: A 429 PHE cc_start: 0.8654 (t80) cc_final: 0.8256 (t80) REVERT: B 104 TRP cc_start: 0.7747 (m-90) cc_final: 0.7524 (m-90) REVERT: B 351 TYR cc_start: 0.8260 (p90) cc_final: 0.8032 (p90) REVERT: B 436 TRP cc_start: 0.8544 (p90) cc_final: 0.8016 (p90) REVERT: B 515 PHE cc_start: 0.8462 (m-80) cc_final: 0.8047 (m-80) REVERT: B 979 ASP cc_start: 0.8916 (t70) cc_final: 0.8680 (t0) REVERT: C 351 TYR cc_start: 0.8370 (p90) cc_final: 0.8152 (p90) REVERT: C 429 PHE cc_start: 0.8679 (t80) cc_final: 0.8291 (t80) REVERT: C 436 TRP cc_start: 0.8728 (p90) cc_final: 0.8301 (p90) outliers start: 38 outliers final: 26 residues processed: 211 average time/residue: 0.1435 time to fit residues: 51.9723 Evaluate side-chains 203 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 108 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 256 optimal weight: 0.0470 chunk 280 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 chunk 139 optimal weight: 30.0000 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN B 196 ASN C 613 GLN C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080970 restraints weight = 48536.109| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.27 r_work: 0.2806 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25344 Z= 0.121 Angle : 0.611 11.896 34599 Z= 0.303 Chirality : 0.047 0.329 4080 Planarity : 0.004 0.039 4368 Dihedral : 4.133 27.803 3258 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.32 % Allowed : 9.73 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3003 helix: 2.07 (0.21), residues: 624 sheet: 0.40 (0.18), residues: 699 loop : -0.61 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.021 0.001 TYR A1138 PHE 0.020 0.001 PHE C 515 TRP 0.018 0.001 TRP A 104 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (25242) covalent geometry : angle 0.56497 / 0.29 (34332) SS BOND : bond 0.00348 / 0.21 ( 39) SS BOND : angle 2.18810 / 1.41 ( 78) hydrogen bonds : bond 0.03671 / 2.46 ( 1005) hydrogen bonds : angle 5.37108 / 3.71 ( 2898) link_BETA1-4 : bond 0.00327 / 0.18 ( 15) link_BETA1-4 : angle 0.82818 / 0.57 ( 45) link_NAG-ASN : bond 0.00690 / 0.49 ( 48) link_NAG-ASN : angle 3.30221 / 2.19 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7264 (p90) cc_final: 0.6699 (p90) REVERT: A 351 TYR cc_start: 0.8408 (p90) cc_final: 0.8153 (p90) REVERT: A 378 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8320 (ttpp) REVERT: A 429 PHE cc_start: 0.8620 (t80) cc_final: 0.8199 (t80) REVERT: A 964 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8701 (mttp) REVERT: B 104 TRP cc_start: 0.7690 (m-90) cc_final: 0.7453 (m-90) REVERT: B 351 TYR cc_start: 0.8228 (p90) cc_final: 0.8013 (p90) REVERT: B 436 TRP cc_start: 0.8488 (p90) cc_final: 0.7966 (p90) REVERT: B 979 ASP cc_start: 0.8930 (t70) cc_final: 0.8684 (t0) REVERT: C 351 TYR cc_start: 0.8450 (p90) cc_final: 0.8222 (p90) REVERT: C 429 PHE cc_start: 0.8658 (t80) cc_final: 0.8198 (t80) REVERT: C 434 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8646 (mm) REVERT: C 436 TRP cc_start: 0.8695 (p90) cc_final: 0.8224 (p90) REVERT: C 990 GLU cc_start: 0.8270 (pm20) cc_final: 0.7904 (pm20) outliers start: 35 outliers final: 19 residues processed: 222 average time/residue: 0.1433 time to fit residues: 54.6718 Evaluate side-chains 205 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 101 optimal weight: 10.0000 chunk 275 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 394 ASN B 919 ASN B 957 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.131547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.077400 restraints weight = 48900.134| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.06 r_work: 0.2771 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25344 Z= 0.235 Angle : 0.649 11.641 34599 Z= 0.322 Chirality : 0.048 0.319 4080 Planarity : 0.004 0.040 4368 Dihedral : 4.215 28.626 3258 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.39 % Allowed : 10.56 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3003 helix: 1.84 (0.21), residues: 636 sheet: 0.28 (0.18), residues: 720 loop : -0.65 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.019 0.001 TYR A 495 PHE 0.020 0.001 PHE C 515 TRP 0.018 0.001 TRP C 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (25242) covalent geometry : angle 0.60740 / 0.31 (34332) SS BOND : bond 0.00611 / 0.35 ( 39) SS BOND : angle 2.13736 / 1.40 ( 78) hydrogen bonds : bond 0.04020 / 2.70 ( 1005) hydrogen bonds : angle 5.44038 / 3.75 ( 2898) link_BETA1-4 : bond 0.00225 / 0.13 ( 15) link_BETA1-4 : angle 0.88197 / 0.61 ( 45) link_NAG-ASN : bond 0.00643 / 0.45 ( 48) link_NAG-ASN : angle 3.25310 / 2.15 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7254 (p90) cc_final: 0.6646 (p90) REVERT: A 351 TYR cc_start: 0.8472 (p90) cc_final: 0.8229 (p90) REVERT: A 378 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8386 (ttpp) REVERT: A 429 PHE cc_start: 0.8642 (t80) cc_final: 0.8245 (t80) REVERT: A 436 TRP cc_start: 0.8772 (p90) cc_final: 0.8392 (p90) REVERT: A 964 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8697 (mttp) REVERT: B 52 GLN cc_start: 0.9077 (tt0) cc_final: 0.8605 (tm-30) REVERT: B 436 TRP cc_start: 0.8509 (p90) cc_final: 0.7969 (p90) REVERT: B 979 ASP cc_start: 0.8962 (t70) cc_final: 0.8700 (t0) REVERT: C 351 TYR cc_start: 0.8460 (p90) cc_final: 0.8229 (p90) REVERT: C 429 PHE cc_start: 0.8669 (t80) cc_final: 0.8223 (t80) REVERT: C 434 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8700 (mm) REVERT: C 436 TRP cc_start: 0.8734 (p90) cc_final: 0.8284 (p90) REVERT: C 990 GLU cc_start: 0.8244 (pm20) cc_final: 0.7954 (pm20) outliers start: 37 outliers final: 25 residues processed: 208 average time/residue: 0.1436 time to fit residues: 51.1289 Evaluate side-chains 199 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 281 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN ** C 544 ASN ** 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 = 0.3916 r_free = 0.3916 target = 0.131308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.077277 restraints weight = 48799.257| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.28 r_work: 0.2727 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 25344 Z= 0.276 Angle : 0.670 11.604 34599 Z= 0.333 Chirality : 0.048 0.314 4080 Planarity : 0.004 0.040 4368 Dihedral : 4.320 29.182 3258 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.05 % Allowed : 10.94 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3003 helix: 1.73 (0.21), residues: 633 sheet: 0.20 (0.18), residues: 720 loop : -0.71 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1014 TYR 0.018 0.001 TYR A1067 PHE 0.020 0.002 PHE C 515 TRP 0.028 0.002 TRP C 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (25242) covalent geometry : angle 0.63010 / 0.32 (34332) SS BOND : bond 0.00689 / 0.40 ( 39) SS BOND : angle 2.14907 / 1.41 ( 78) hydrogen bonds : bond 0.04205 / 2.83 ( 1005) hydrogen bonds : angle 5.50595 / 3.80 ( 2898) link_BETA1-4 : bond 0.00199 / 0.11 ( 15) link_BETA1-4 : angle 0.91583 / 0.62 ( 45) link_NAG-ASN : bond 0.00642 / 0.45 ( 48) link_NAG-ASN : angle 3.20912 / 2.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7216 (p90) cc_final: 0.6538 (p90) REVERT: A 351 TYR cc_start: 0.8544 (p90) cc_final: 0.8292 (p90) REVERT: A 378 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8327 (ttpp) REVERT: A 429 PHE cc_start: 0.8683 (t80) cc_final: 0.8330 (t80) REVERT: A 436 TRP cc_start: 0.8726 (p90) cc_final: 0.8312 (p90) REVERT: A 964 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8974 (ttmm) REVERT: B 52 GLN cc_start: 0.9104 (tt0) cc_final: 0.8643 (tm-30) REVERT: B 351 TYR cc_start: 0.8103 (p90) cc_final: 0.7849 (p90) REVERT: B 436 TRP cc_start: 0.8461 (p90) cc_final: 0.7866 (p90) REVERT: B 964 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8910 (ttmm) REVERT: C 351 TYR cc_start: 0.8552 (p90) cc_final: 0.8329 (p90) REVERT: C 429 PHE cc_start: 0.8687 (t80) cc_final: 0.8237 (t80) REVERT: C 434 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8583 (mm) REVERT: C 436 TRP cc_start: 0.8674 (p90) cc_final: 0.8199 (p90) REVERT: C 990 GLU cc_start: 0.8266 (pm20) cc_final: 0.7937 (pm20) outliers start: 28 outliers final: 25 residues processed: 200 average time/residue: 0.1440 time to fit residues: 48.7924 Evaluate side-chains 195 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 90 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 275 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.131682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077621 restraints weight = 48587.617| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.03 r_work: 0.2774 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 25344 Z= 0.198 Angle : 0.630 11.598 34599 Z= 0.315 Chirality : 0.047 0.316 4080 Planarity : 0.004 0.042 4368 Dihedral : 4.290 29.530 3258 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.16 % Allowed : 10.86 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3003 helix: 1.79 (0.21), residues: 633 sheet: 0.16 (0.18), residues: 720 loop : -0.72 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.027 0.001 TYR C 495 PHE 0.027 0.001 PHE A 133 TRP 0.027 0.002 TRP B 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (25242) covalent geometry : angle 0.59165 / 0.31 (34332) SS BOND : bond 0.00508 / 0.31 ( 39) SS BOND : angle 1.89584 / 1.25 ( 78) hydrogen bonds : bond 0.03950 / 2.65 ( 1005) hydrogen bonds : angle 5.41910 / 3.74 ( 2898) link_BETA1-4 : bond 0.00258 / 0.15 ( 15) link_BETA1-4 : angle 0.88846 / 0.61 ( 45) link_NAG-ASN : bond 0.00630 / 0.44 ( 48) link_NAG-ASN : angle 3.13225 / 2.07 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: A 238 PHE cc_start: 0.7230 (p90) cc_final: 0.6538 (p90) REVERT: A 378 LYS cc_start: 0.8791 (ttpp) cc_final: 0.8590 (ttpp) REVERT: A 429 PHE cc_start: 0.8710 (t80) cc_final: 0.8338 (t80) REVERT: A 436 TRP cc_start: 0.8779 (p90) cc_final: 0.8401 (p90) REVERT: A 725 GLU cc_start: 0.8626 (tt0) cc_final: 0.8424 (tt0) REVERT: A 964 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8733 (mttp) REVERT: B 52 GLN cc_start: 0.9145 (tt0) cc_final: 0.8746 (tm-30) REVERT: B 351 TYR cc_start: 0.8067 (p90) cc_final: 0.7834 (p90) REVERT: B 436 TRP cc_start: 0.8467 (p90) cc_final: 0.8188 (p90) REVERT: C 133 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: C 351 TYR cc_start: 0.8529 (p90) cc_final: 0.8321 (p90) REVERT: C 429 PHE cc_start: 0.8687 (t80) cc_final: 0.8243 (t80) REVERT: C 434 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8619 (mm) REVERT: C 436 TRP cc_start: 0.8686 (p90) cc_final: 0.8254 (p90) REVERT: C 990 GLU cc_start: 0.8239 (pm20) cc_final: 0.7918 (pm20) outliers start: 31 outliers final: 26 residues processed: 199 average time/residue: 0.1439 time to fit residues: 48.7914 Evaluate side-chains 201 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 78 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 282 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 GLN B1002 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079909 restraints weight = 48438.280| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.04 r_work: 0.2823 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25344 Z= 0.119 Angle : 0.602 11.548 34599 Z= 0.301 Chirality : 0.047 0.321 4080 Planarity : 0.004 0.043 4368 Dihedral : 4.168 29.695 3258 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.98 % Allowed : 11.05 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3003 helix: 2.02 (0.21), residues: 624 sheet: 0.29 (0.18), residues: 690 loop : -0.67 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.024 0.001 TYR A 351 PHE 0.020 0.001 PHE C 515 TRP 0.025 0.002 TRP B 104 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25242) covalent geometry : angle 0.56556 / 0.29 (34332) SS BOND : bond 0.00337 / 0.22 ( 39) SS BOND : angle 1.52239 / 1.00 ( 78) hydrogen bonds : bond 0.03574 / 2.39 ( 1005) hydrogen bonds : angle 5.25910 / 3.64 ( 2898) link_BETA1-4 : bond 0.00345 / 0.19 ( 15) link_BETA1-4 : angle 0.87168 / 0.59 ( 45) link_NAG-ASN : bond 0.00648 / 0.46 ( 48) link_NAG-ASN : angle 3.04530 / 2.01 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9009 (tt0) cc_final: 0.8566 (tm-30) REVERT: A 133 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: A 238 PHE cc_start: 0.7201 (p90) cc_final: 0.6554 (p90) REVERT: A 351 TYR cc_start: 0.8349 (p90) cc_final: 0.8054 (p90) REVERT: A 378 LYS cc_start: 0.8791 (ttpp) cc_final: 0.8496 (ttpp) REVERT: A 429 PHE cc_start: 0.8698 (t80) cc_final: 0.8346 (t80) REVERT: A 436 TRP cc_start: 0.8724 (p90) cc_final: 0.8307 (p90) REVERT: A 725 GLU cc_start: 0.9006 (tt0) cc_final: 0.8792 (tt0) REVERT: A 964 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8741 (mttp) REVERT: B 52 GLN cc_start: 0.9251 (tt0) cc_final: 0.8758 (tm-30) REVERT: B 351 TYR cc_start: 0.8019 (p90) cc_final: 0.7798 (p90) REVERT: B 436 TRP cc_start: 0.8443 (p90) cc_final: 0.8149 (p90) REVERT: B 737 ASP cc_start: 0.8188 (t0) cc_final: 0.7978 (t70) REVERT: C 133 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6014 (m-80) REVERT: C 351 TYR cc_start: 0.8532 (p90) cc_final: 0.8320 (p90) REVERT: C 429 PHE cc_start: 0.8725 (t80) cc_final: 0.8252 (t80) REVERT: C 434 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8621 (mm) REVERT: C 436 TRP cc_start: 0.8613 (p90) cc_final: 0.8197 (p90) REVERT: C 990 GLU cc_start: 0.8373 (pm20) cc_final: 0.8061 (pm20) outliers start: 26 outliers final: 22 residues processed: 204 average time/residue: 0.1486 time to fit residues: 51.5416 Evaluate side-chains 206 residues out of total 2661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 166 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 213 optimal weight: 50.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1005 GLN B 957 GLN B1002 GLN ** C 544 ASN ** 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 = 0.3957 r_free = 0.3957 target = 0.134169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080623 restraints weight = 48332.767| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.07 r_work: 0.2827 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25344 Z= 0.118 Angle : 0.591 11.250 34599 Z= 0.295 Chirality : 0.046 0.317 4080 Planarity : 0.004 0.047 4368 Dihedral : 4.092 29.921 3258 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.13 % Allowed : 11.12 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3003 helix: 2.17 (0.21), residues: 624 sheet: 0.35 (0.18), residues: 723 loop : -0.63 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 214 TYR 0.027 0.001 TYR A 495 PHE 0.019 0.001 PHE C 515 TRP 0.023 0.002 TRP C 104 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (25242) covalent geometry : angle 0.55649 / 0.29 (34332) SS BOND : bond 0.00346 / 0.23 ( 39) SS BOND : angle 1.45472 / 0.96 ( 78) hydrogen bonds : bond 0.03465 / 2.32 ( 1005) hydrogen bonds : angle 5.17350 / 3.58 ( 2898) link_BETA1-4 : bond 0.00317 / 0.18 ( 15) link_BETA1-4 : angle 0.86752 / 0.59 ( 45) link_NAG-ASN : bond 0.00642 / 0.45 ( 48) link_NAG-ASN : angle 2.96227 / 1.95 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6458.77 seconds wall clock time: 111 minutes 31.77 seconds (6691.77 seconds total)