Starting phenix.real_space_refine on Sun Jul 5 10:40:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z9r_14576/07_2026/7z9r_14576.cif" } resolution = 4.2 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= 0.003 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 120 5.16 5 C 17221 2.51 5 N 4415 2.21 5 O 5322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27078 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7719 Classifications: {'peptide': 988} Link IDs: {'PTRANS': 49, 'TRANS': 938} Chain breaks: 9 Chain: "B" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7745 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Chain: "C" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7738 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Z" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.11, per 1000 atoms: 0.23 Number of scatterers: 27078 At special positions: 0 Unit cell: (130.784, 139.36, 216.544, 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 120 16.00 O 5322 8.00 N 4415 7.00 C 17221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.91 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 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=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.07 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.01 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.01 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 709 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6246 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 55 sheets defined 24.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.981A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.335A 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 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: 3.540A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.681A 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: 4.237A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.941A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.599A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.025A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.339A 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 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 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: 4.040A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.874A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.583A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.762A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.518A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.594A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.809A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.966A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.355A 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 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.574A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.642A 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: 4.371A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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: 3.680A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.944A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.111A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.955A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.671A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.573A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.456A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.064A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.001A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.776A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.987A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.191A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.797A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.328A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.308A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.731A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.709A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.448A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.627A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.006A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.988A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.777A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.344A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.699A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.556A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.669A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.917A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.550A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.882A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.977A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.001A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.712A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.166A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.574A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.288A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.288A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.293A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.293A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3021 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: 7.40 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5965 1.33 - 1.46: 9667 1.46 - 1.59: 11885 1.59 - 1.72: 0 1.72 - 1.85: 153 Bond restraints: 27670 Sorted by residual: bond pdb=" C ASP C 138 " pdb=" N PRO C 139 " ideal model delta sigma weight residual 1.333 1.384 -0.051 1.17e-02 7.31e+03 1.89e+01 bond pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.333 1.383 -0.050 1.17e-02 7.31e+03 1.84e+01 bond pdb=" CE1 HIS C1064 " pdb=" NE2 HIS C1064 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.57e+01 bond pdb=" N ASN A 81 " pdb=" CA ASN A 81 " ideal model delta sigma weight residual 1.458 1.533 -0.075 1.90e-02 2.77e+03 1.56e+01 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.331 1.381 -0.051 1.31e-02 5.83e+03 1.49e+01 ... (remaining 27665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 35532 2.72 - 5.44: 1958 5.44 - 8.16: 117 8.16 - 10.88: 15 10.88 - 13.60: 3 Bond angle restraints: 37625 Sorted by residual: angle pdb=" C CYS A 166 " pdb=" CA CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sigma weight residual 112.05 99.52 12.53 1.52e+00 4.33e-01 6.79e+01 angle pdb=" C PHE C 329 " pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " ideal model delta sigma weight residual 109.22 120.23 -11.01 1.52e+00 4.33e-01 5.24e+01 angle pdb=" N SER B1147 " pdb=" CA SER B1147 " pdb=" CB SER B1147 " ideal model delta sigma weight residual 110.50 120.69 -10.19 1.70e+00 3.46e-01 3.60e+01 angle pdb=" N ASN B1108 " pdb=" CA ASN B1108 " pdb=" C ASN B1108 " ideal model delta sigma weight residual 111.82 118.77 -6.95 1.16e+00 7.43e-01 3.59e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.00e+00 1.00e+00 3.58e+01 ... (remaining 37620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14771 17.80 - 35.59: 871 35.59 - 53.39: 168 53.39 - 71.19: 57 71.19 - 88.98: 26 Dihedral angle restraints: 15893 sinusoidal: 6166 harmonic: 9727 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -174.98 88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 171.46 -78.46 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 15890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3793 0.144 - 0.288: 582 0.288 - 0.431: 51 0.431 - 0.575: 9 0.575 - 0.719: 2 Chirality restraints: 4437 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.07e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 2.02e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 ... (remaining 4434 not shown) Planarity restraints: 4808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " 0.363 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG P 1 " -0.094 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.354 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG M 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1305 " -0.345 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C1305 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C1305 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C1305 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG C1305 " -0.099 2.00e-02 2.50e+03 ... (remaining 4805 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 1 1.93 - 2.67: 476 2.67 - 3.41: 35695 3.41 - 4.16: 67112 4.16 - 4.90: 116021 Nonbonded interactions: 219305 Sorted by model distance: nonbonded pdb=" OE1 GLU A 281 " pdb=" OD1 ASN A 282 " model vdw 1.182 3.040 nonbonded pdb=" SG CYS A 131 " pdb=" CA CYS A 166 " model vdw 1.927 3.064 nonbonded pdb=" O GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 1.941 3.040 nonbonded pdb=" O THR A 333 " pdb=" OD1 ASN A 334 " model vdw 1.984 3.040 nonbonded pdb=" OD1 ASN C 137 " pdb=" N ASP C 138 " model vdw 2.047 3.120 ... (remaining 219300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 263 or resid 265 through 676 or resid 690 through 827 \ or resid 856 through 1307)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 196 or resid 200 through 211 or resid 215 through 263 or resid 265 through 827 \ or resid 856 through 1307)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 196 or resid 200 through 211 or resid 215 through 1307 \ )) } 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.650 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.008 0.120 27774 Z= 0.524 Angle : 1.458 50.025 37895 Z= 0.910 Chirality : 0.105 0.719 4437 Planarity : 0.023 0.310 4766 Dihedral : 12.856 88.199 9521 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.21 % Allowed : 4.62 % Favored : 94.17 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3289 helix: -0.33 (0.19), residues: 678 sheet: -0.16 (0.17), residues: 798 loop : -1.21 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG C1091 TYR 0.058 0.007 TYR B 365 PHE 0.052 0.008 PHE B 565 TRP 0.037 0.006 TRP B 353 HIS 0.033 0.007 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.52 (27670) covalent geometry : angle 1.39512 / 0.90 (37625) SS BOND : bond 0.02332 / 1.59 ( 42) SS BOND : angle 6.31250 / 3.54 ( 84) hydrogen bonds : bond 0.14379 / 9.39 ( 1128) hydrogen bonds : angle 7.15917 / 5.00 ( 3021) link_BETA1-4 : bond 0.00370 / 0.24 ( 20) link_BETA1-4 : angle 1.55879 / 1.01 ( 60) link_NAG-ASN : bond 0.01287 / 0.82 ( 42) link_NAG-ASN : angle 5.50371 / 3.96 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 602 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7485 (p) REVERT: A 55 PHE cc_start: 0.8308 (m-80) cc_final: 0.7904 (m-80) REVERT: A 108 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6677 (t) REVERT: A 277 LEU cc_start: 0.8823 (mt) cc_final: 0.8622 (mm) REVERT: A 319 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7303 (mtp-110) REVERT: A 326 ILE cc_start: 0.7560 (mt) cc_final: 0.7229 (pt) REVERT: A 347 PHE cc_start: 0.7691 (m-80) cc_final: 0.6560 (m-80) REVERT: A 355 ARG cc_start: 0.6656 (ttm170) cc_final: 0.6228 (mtp85) REVERT: A 511 VAL cc_start: 0.6728 (t) cc_final: 0.6302 (m) REVERT: A 565 PHE cc_start: 0.8493 (p90) cc_final: 0.8241 (p90) REVERT: A 658 ASN cc_start: 0.8033 (m-40) cc_final: 0.7266 (t0) REVERT: A 666 ILE cc_start: 0.9133 (mt) cc_final: 0.8884 (mp) REVERT: A 758 SER cc_start: 0.8440 (m) cc_final: 0.8160 (p) REVERT: A 825 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7890 (mtmt) REVERT: A 1041 ASP cc_start: 0.9072 (m-30) cc_final: 0.8570 (t0) REVERT: A 1050 MET cc_start: 0.7821 (ptt) cc_final: 0.7434 (ptp) REVERT: A 1139 ASP cc_start: 0.8379 (t0) cc_final: 0.8013 (t0) REVERT: B 41 LYS cc_start: 0.6821 (mttm) cc_final: 0.6351 (mmtp) REVERT: B 53 ASP cc_start: 0.7882 (t0) cc_final: 0.7588 (t0) REVERT: B 223 LEU cc_start: 0.8527 (mp) cc_final: 0.8286 (mp) REVERT: B 266 TYR cc_start: 0.9034 (m-80) cc_final: 0.8564 (m-80) REVERT: B 347 PHE cc_start: 0.8055 (m-80) cc_final: 0.7494 (m-10) REVERT: B 389 ASP cc_start: 0.7927 (m-30) cc_final: 0.7406 (t0) REVERT: B 420 ASP cc_start: 0.8342 (m-30) cc_final: 0.8012 (m-30) REVERT: B 442 ASP cc_start: 0.7035 (m-30) cc_final: 0.6559 (m-30) REVERT: B 493 GLN cc_start: 0.7815 (tt0) cc_final: 0.7370 (tm-30) REVERT: B 532 ASN cc_start: 0.8336 (m-40) cc_final: 0.8117 (t0) REVERT: B 558 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7596 (mttt) REVERT: B 663 ASP cc_start: 0.9063 (t0) cc_final: 0.8775 (m-30) REVERT: B 698 SER cc_start: 0.8528 (t) cc_final: 0.7913 (p) REVERT: B 702 GLU cc_start: 0.8671 (tt0) cc_final: 0.8399 (tt0) REVERT: B 748 GLU cc_start: 0.7862 (mp0) cc_final: 0.7632 (mt-10) REVERT: B 825 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7681 (tptt) REVERT: B 868 GLU cc_start: 0.8385 (pt0) cc_final: 0.7714 (tm-30) REVERT: B 895 GLN cc_start: 0.9219 (pm20) cc_final: 0.8804 (pm20) REVERT: B 968 SER cc_start: 0.9343 (m) cc_final: 0.8584 (p) REVERT: B 997 ILE cc_start: 0.8870 (mt) cc_final: 0.8647 (mt) REVERT: B 1050 MET cc_start: 0.8613 (ptt) cc_final: 0.8396 (ptp) REVERT: B 1066 THR cc_start: 0.9589 (p) cc_final: 0.9328 (t) REVERT: B 1097 SER cc_start: 0.8757 (t) cc_final: 0.8399 (p) REVERT: C 44 ARG cc_start: 0.6981 (mtt90) cc_final: 0.6760 (mtt90) REVERT: C 88 ASP cc_start: 0.8095 (m-30) cc_final: 0.7551 (t70) REVERT: C 169 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7482 (mp0) REVERT: C 201 PHE cc_start: 0.7780 (t80) cc_final: 0.7576 (t80) REVERT: C 565 PHE cc_start: 0.8120 (p90) cc_final: 0.7916 (p90) REVERT: C 697 MET cc_start: 0.8831 (ptm) cc_final: 0.8522 (ptm) REVERT: C 773 GLU cc_start: 0.8322 (tt0) cc_final: 0.8087 (tp30) REVERT: C 780 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8830 (tp30) REVERT: C 819 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8348 (mt-10) REVERT: C 1100 THR cc_start: 0.7740 (p) cc_final: 0.7457 (p) REVERT: C 1101 HIS cc_start: 0.7453 (m90) cc_final: 0.7197 (m90) REVERT: C 1135 ASN cc_start: 0.5914 (t0) cc_final: 0.5455 (t0) REVERT: Y 36 TRP cc_start: 0.5928 (m100) cc_final: 0.5251 (m100) REVERT: Y 62 ASP cc_start: 0.6673 (m-30) cc_final: 0.6189 (p0) REVERT: Y 79 VAL cc_start: 0.7463 (p) cc_final: 0.6458 (m) REVERT: Y 88 TYR cc_start: 0.7292 (t80) cc_final: 0.6980 (m-10) REVERT: Y 105 LEU cc_start: 0.8029 (tp) cc_final: 0.7711 (tp) REVERT: Z 34 MET cc_start: 0.3444 (mmm) cc_final: 0.2728 (ppp) REVERT: Z 83 MET cc_start: -0.2953 (mtp) cc_final: -0.3187 (mtp) outliers start: 35 outliers final: 4 residues processed: 625 average time/residue: 0.1815 time to fit residues: 177.4725 Evaluate side-chains 257 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 251 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN A 81 ASN A 164 ASN A 563 GLN A 564 GLN A 784 GLN A 804 GLN A 935 GLN A 957 GLN A1011 GLN A1071 GLN B 234 ASN B 506 GLN B 519 HIS B 613 GLN B1048 HIS B1071 GLN C 81 ASN C 125 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 607 GLN C 655 HIS C 762 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1048 HIS Y 3 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104445 restraints weight = 61031.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101916 restraints weight = 49393.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.102493 restraints weight = 43463.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103259 restraints weight = 36254.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103418 restraints weight = 32021.519| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 27774 Z= 0.146 Angle : 0.707 13.468 37895 Z= 0.344 Chirality : 0.047 0.267 4437 Planarity : 0.004 0.051 4766 Dihedral : 4.727 29.025 3600 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.24 % Allowed : 2.62 % Favored : 97.14 % 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: -0.24 (0.14), residues: 3289 helix: 0.91 (0.20), residues: 682 sheet: 0.02 (0.17), residues: 757 loop : -0.61 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1091 TYR 0.026 0.001 TYR C 369 PHE 0.039 0.002 PHE B 565 TRP 0.024 0.001 TRP C 64 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (27670) covalent geometry : angle 0.68193 / 0.34 (37625) SS BOND : bond 0.00908 / 0.40 ( 42) SS BOND : angle 2.17962 / 1.48 ( 84) hydrogen bonds : bond 0.04760 / 3.06 ( 1128) hydrogen bonds : angle 5.82324 / 4.10 ( 3021) link_BETA1-4 : bond 0.00364 / 0.23 ( 20) link_BETA1-4 : angle 1.50573 / 1.00 ( 60) link_NAG-ASN : bond 0.00461 / 0.32 ( 42) link_NAG-ASN : angle 2.66261 / 1.85 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 386 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9118 (tp) cc_final: 0.8880 (tp) REVERT: A 101 ILE cc_start: 0.9110 (pt) cc_final: 0.8809 (tp) REVERT: A 287 ASP cc_start: 0.8239 (t0) cc_final: 0.8030 (m-30) REVERT: A 347 PHE cc_start: 0.6599 (m-80) cc_final: 0.5806 (m-10) REVERT: A 365 TYR cc_start: 0.8183 (m-80) cc_final: 0.7862 (m-10) REVERT: A 544 ASN cc_start: 0.8461 (m-40) cc_final: 0.7938 (m-40) REVERT: A 699 LEU cc_start: 0.9059 (mt) cc_final: 0.8813 (mt) REVERT: A 1041 ASP cc_start: 0.7490 (m-30) cc_final: 0.7259 (t0) REVERT: B 41 LYS cc_start: 0.7465 (mttm) cc_final: 0.7249 (mttm) REVERT: B 188 ASN cc_start: 0.7770 (t0) cc_final: 0.7506 (m-40) REVERT: B 241 LEU cc_start: 0.7978 (mt) cc_final: 0.7723 (tp) REVERT: B 357 ARG cc_start: 0.7460 (ttp80) cc_final: 0.7220 (mtp180) REVERT: B 508 TYR cc_start: 0.7758 (m-80) cc_final: 0.7047 (m-80) REVERT: B 558 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7414 (mttt) REVERT: B 708 SER cc_start: 0.9332 (p) cc_final: 0.8931 (m) REVERT: B 825 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7992 (tppt) REVERT: B 968 SER cc_start: 0.9491 (m) cc_final: 0.9086 (p) REVERT: B 1097 SER cc_start: 0.9236 (t) cc_final: 0.8762 (p) REVERT: C 204 TYR cc_start: 0.7696 (m-80) cc_final: 0.7381 (m-80) REVERT: C 313 TYR cc_start: 0.8806 (m-80) cc_final: 0.8539 (m-80) REVERT: C 533 LEU cc_start: 0.5999 (pp) cc_final: 0.5284 (mt) REVERT: C 734 THR cc_start: 0.9092 (m) cc_final: 0.8767 (t) REVERT: C 819 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8476 (mt-10) REVERT: C 900 MET cc_start: 0.8223 (mtp) cc_final: 0.7686 (mtm) REVERT: Y 94 TYR cc_start: 0.5047 (m-80) cc_final: 0.4651 (m-10) REVERT: Y 105 LEU cc_start: 0.8458 (tp) cc_final: 0.8199 (tp) outliers start: 7 outliers final: 4 residues processed: 393 average time/residue: 0.1533 time to fit residues: 99.2578 Evaluate side-chains 207 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 51 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 268 optimal weight: 0.7980 chunk 254 optimal weight: 0.1980 chunk 252 optimal weight: 3.9990 chunk 232 optimal weight: 30.0000 chunk 21 optimal weight: 0.0170 chunk 231 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 overall best weight: 1.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1142 GLN B 239 GLN B 762 GLN B 787 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 81 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096729 restraints weight = 63697.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096360 restraints weight = 58809.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096689 restraints weight = 47610.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097191 restraints weight = 39787.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097488 restraints weight = 34508.724| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27774 Z= 0.171 Angle : 0.660 10.985 37895 Z= 0.330 Chirality : 0.046 0.268 4437 Planarity : 0.004 0.049 4766 Dihedral : 4.629 53.855 3600 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.14 % Allowed : 3.14 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.03 (0.14), residues: 3289 helix: 1.29 (0.20), residues: 678 sheet: 0.20 (0.17), residues: 790 loop : -0.52 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1107 TYR 0.033 0.001 TYR A 904 PHE 0.018 0.001 PHE A 823 TRP 0.018 0.001 TRP C 64 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (27670) covalent geometry : angle 0.63824 / 0.32 (37625) SS BOND : bond 0.00429 / 0.26 ( 42) SS BOND : angle 2.25391 / 1.60 ( 84) hydrogen bonds : bond 0.04549 / 2.92 ( 1128) hydrogen bonds : angle 5.56662 / 3.92 ( 3021) link_BETA1-4 : bond 0.00216 / 0.15 ( 20) link_BETA1-4 : angle 1.37686 / 0.93 ( 60) link_NAG-ASN : bond 0.00352 / 0.22 ( 42) link_NAG-ASN : angle 2.28984 / 1.57 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 301 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6389 (m-80) cc_final: 0.5781 (m-10) REVERT: A 365 TYR cc_start: 0.8114 (m-80) cc_final: 0.7824 (m-10) REVERT: A 387 LEU cc_start: 0.9017 (mp) cc_final: 0.8742 (mp) REVERT: B 30 ASN cc_start: 0.8668 (t0) cc_final: 0.8389 (m110) REVERT: B 188 ASN cc_start: 0.7765 (t0) cc_final: 0.7560 (m-40) REVERT: B 508 TYR cc_start: 0.7527 (m-80) cc_final: 0.7279 (m-10) REVERT: B 558 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7287 (mmtt) REVERT: B 825 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7938 (tppt) REVERT: B 968 SER cc_start: 0.9487 (m) cc_final: 0.9161 (p) REVERT: C 106 PHE cc_start: 0.7906 (m-80) cc_final: 0.7660 (m-80) REVERT: C 313 TYR cc_start: 0.8884 (m-80) cc_final: 0.8608 (m-80) REVERT: C 533 LEU cc_start: 0.6171 (pp) cc_final: 0.5417 (mt) REVERT: C 734 THR cc_start: 0.9116 (m) cc_final: 0.8878 (t) REVERT: C 819 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8595 (mt-10) REVERT: Y 12 MET cc_start: 0.4565 (ttm) cc_final: 0.3980 (ttm) REVERT: Y 79 VAL cc_start: 0.7164 (p) cc_final: 0.6369 (m) REVERT: Y 94 TYR cc_start: 0.4472 (m-80) cc_final: 0.4054 (m-10) REVERT: Y 105 LEU cc_start: 0.8700 (tp) cc_final: 0.8471 (tp) outliers start: 4 outliers final: 1 residues processed: 303 average time/residue: 0.1521 time to fit residues: 76.3853 Evaluate side-chains 192 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 87 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 121 optimal weight: 8.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 317 ASN A1010 GLN B 207 HIS B 239 GLN B 394 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.135599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096707 restraints weight = 62225.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096676 restraints weight = 56054.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097055 restraints weight = 41251.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097538 restraints weight = 34679.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097674 restraints weight = 30340.604| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27774 Z= 0.125 Angle : 0.589 11.395 37895 Z= 0.294 Chirality : 0.045 0.249 4437 Planarity : 0.004 0.048 4766 Dihedral : 4.347 36.882 3600 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.10 % Allowed : 2.03 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.24 (0.14), residues: 3289 helix: 1.63 (0.21), residues: 669 sheet: 0.34 (0.17), residues: 805 loop : -0.46 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.022 0.001 TYR A1067 PHE 0.025 0.001 PHE B 392 TRP 0.015 0.001 TRP Z 53 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (27670) covalent geometry : angle 0.57139 / 0.29 (37625) SS BOND : bond 0.00374 / 0.23 ( 42) SS BOND : angle 1.91296 / 1.33 ( 84) hydrogen bonds : bond 0.04099 / 2.63 ( 1128) hydrogen bonds : angle 5.33252 / 3.77 ( 3021) link_BETA1-4 : bond 0.00234 / 0.16 ( 20) link_BETA1-4 : angle 1.13617 / 0.77 ( 60) link_NAG-ASN : bond 0.00259 / 0.18 ( 42) link_NAG-ASN : angle 1.90130 / 1.33 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6368 (m-80) cc_final: 0.5717 (m-10) REVERT: A 365 TYR cc_start: 0.8092 (m-80) cc_final: 0.7878 (m-10) REVERT: A 387 LEU cc_start: 0.9008 (mp) cc_final: 0.8743 (mp) REVERT: A 690 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6330 (pm20) REVERT: A 698 SER cc_start: 0.9308 (t) cc_final: 0.9045 (p) REVERT: A 699 LEU cc_start: 0.8996 (mt) cc_final: 0.8753 (mt) REVERT: B 30 ASN cc_start: 0.8559 (t0) cc_final: 0.8325 (m-40) REVERT: B 400 PHE cc_start: 0.7645 (p90) cc_final: 0.7391 (p90) REVERT: B 468 ILE cc_start: 0.8731 (pt) cc_final: 0.8300 (mm) REVERT: B 558 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7507 (mmtt) REVERT: B 825 LYS cc_start: 0.8311 (mmtt) cc_final: 0.8080 (tppt) REVERT: B 968 SER cc_start: 0.9484 (m) cc_final: 0.9181 (p) REVERT: C 204 TYR cc_start: 0.7779 (m-80) cc_final: 0.7489 (m-80) REVERT: C 313 TYR cc_start: 0.8812 (m-80) cc_final: 0.8577 (m-80) REVERT: C 734 THR cc_start: 0.9122 (m) cc_final: 0.8916 (p) REVERT: C 819 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 935 GLN cc_start: 0.8662 (tt0) cc_final: 0.8350 (tt0) REVERT: Y 34 MET cc_start: 0.6981 (tpp) cc_final: 0.6228 (mtm) REVERT: Y 105 LEU cc_start: 0.8734 (tp) cc_final: 0.8415 (tp) outliers start: 3 outliers final: 0 residues processed: 292 average time/residue: 0.1453 time to fit residues: 72.0012 Evaluate side-chains 187 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 300 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 315 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 32 optimal weight: 20.0000 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 317 ASN A 655 HIS B 207 HIS B 239 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 239 GLN C 450 ASN C 901 GLN C 955 ASN C 965 GLN Y 77 ASN Y 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.125991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088524 restraints weight = 63932.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.088244 restraints weight = 53084.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.088777 restraints weight = 43100.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.089071 restraints weight = 35863.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089133 restraints weight = 32202.411| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 27774 Z= 0.338 Angle : 0.859 12.141 37895 Z= 0.431 Chirality : 0.052 0.298 4437 Planarity : 0.006 0.067 4766 Dihedral : 5.314 38.066 3600 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.46 (0.14), residues: 3289 helix: 0.66 (0.20), residues: 666 sheet: 0.12 (0.17), residues: 819 loop : -0.86 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1107 TYR 0.030 0.002 TYR A 904 PHE 0.042 0.003 PHE B 559 TRP 0.018 0.003 TRP C 886 HIS 0.018 0.003 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.34 (27670) covalent geometry : angle 0.83713 / 0.42 (37625) SS BOND : bond 0.01099 / 0.59 ( 42) SS BOND : angle 2.49901 / 1.72 ( 84) hydrogen bonds : bond 0.05843 / 3.77 ( 1128) hydrogen bonds : angle 6.02847 / 4.20 ( 3021) link_BETA1-4 : bond 0.00469 / 0.32 ( 20) link_BETA1-4 : angle 1.73953 / 1.13 ( 60) link_NAG-ASN : bond 0.00713 / 0.49 ( 42) link_NAG-ASN : angle 2.62900 / 1.81 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8923 (tp) cc_final: 0.8583 (tp) REVERT: A 102 ARG cc_start: 0.7739 (ptt180) cc_final: 0.7142 (mtm180) REVERT: A 347 PHE cc_start: 0.6568 (m-80) cc_final: 0.5989 (m-10) REVERT: A 428 ASP cc_start: 0.7601 (p0) cc_final: 0.6968 (t0) REVERT: A 896 ILE cc_start: 0.9603 (tt) cc_final: 0.9328 (pt) REVERT: B 52 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 118 LEU cc_start: 0.8575 (tt) cc_final: 0.8316 (mm) REVERT: B 239 GLN cc_start: 0.5671 (tp-100) cc_final: 0.5390 (tp40) REVERT: B 468 ILE cc_start: 0.8910 (pt) cc_final: 0.8633 (mm) REVERT: B 549 THR cc_start: 0.9080 (m) cc_final: 0.8840 (p) REVERT: B 558 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7614 (mttt) REVERT: B 825 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8125 (tttp) REVERT: Y 79 VAL cc_start: 0.7416 (p) cc_final: 0.6731 (m) REVERT: Z 34 MET cc_start: 0.1302 (ppp) cc_final: 0.0319 (ttm) outliers start: 3 outliers final: 1 residues processed: 235 average time/residue: 0.1546 time to fit residues: 60.4446 Evaluate side-chains 158 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 166 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 111 optimal weight: 0.0370 chunk 198 optimal weight: 1.9990 chunk 301 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 310 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 297 optimal weight: 9.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.132069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.094440 restraints weight = 62957.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093890 restraints weight = 56694.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094330 restraints weight = 43418.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.094864 restraints weight = 36299.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095109 restraints weight = 31361.282| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27774 Z= 0.122 Angle : 0.606 13.041 37895 Z= 0.307 Chirality : 0.045 0.263 4437 Planarity : 0.004 0.055 4766 Dihedral : 4.593 36.164 3600 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.04 (0.14), residues: 3289 helix: 1.36 (0.21), residues: 650 sheet: 0.28 (0.17), residues: 801 loop : -0.66 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 357 TYR 0.024 0.001 TYR A 904 PHE 0.025 0.001 PHE A 823 TRP 0.016 0.001 TRP C 64 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (27670) covalent geometry : angle 0.58826 / 0.30 (37625) SS BOND : bond 0.00347 / 0.21 ( 42) SS BOND : angle 2.24835 / 1.61 ( 84) hydrogen bonds : bond 0.04316 / 2.77 ( 1128) hydrogen bonds : angle 5.50390 / 3.87 ( 3021) link_BETA1-4 : bond 0.00329 / 0.21 ( 20) link_BETA1-4 : angle 1.02973 / 0.71 ( 60) link_NAG-ASN : bond 0.00223 / 0.15 ( 42) link_NAG-ASN : angle 1.84326 / 1.29 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7706 (ptt180) cc_final: 0.7272 (mtm180) REVERT: A 347 PHE cc_start: 0.6550 (m-80) cc_final: 0.5977 (m-10) REVERT: A 690 GLN cc_start: 0.6519 (mm-40) cc_final: 0.5945 (pm20) REVERT: A 904 TYR cc_start: 0.8057 (m-80) cc_final: 0.7121 (m-10) REVERT: A 955 ASN cc_start: 0.8991 (m-40) cc_final: 0.8681 (t0) REVERT: B 118 LEU cc_start: 0.8631 (tt) cc_final: 0.8264 (mt) REVERT: B 465 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7768 (tm-30) REVERT: B 468 ILE cc_start: 0.8876 (pt) cc_final: 0.8670 (mm) REVERT: B 549 THR cc_start: 0.9092 (m) cc_final: 0.8797 (p) REVERT: B 558 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7588 (mttt) REVERT: B 825 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8102 (tttt) REVERT: Y 34 MET cc_start: 0.7337 (tpp) cc_final: 0.6407 (mtm) REVERT: Y 74 LYS cc_start: 0.6758 (ptmm) cc_final: 0.6525 (pttt) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1566 time to fit residues: 68.9163 Evaluate side-chains 174 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 15 optimal weight: 9.9990 chunk 254 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 187 optimal weight: 0.0870 chunk 313 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 935 GLN A 957 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 762 GLN B 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 955 ASN Y 122 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102247 restraints weight = 62925.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102008 restraints weight = 51331.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102285 restraints weight = 40082.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102770 restraints weight = 35035.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102847 restraints weight = 30939.323| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27774 Z= 0.128 Angle : 0.589 12.090 37895 Z= 0.297 Chirality : 0.044 0.265 4437 Planarity : 0.004 0.061 4766 Dihedral : 4.417 34.914 3600 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.03 % Allowed : 0.86 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.07 (0.14), residues: 3289 helix: 1.48 (0.21), residues: 654 sheet: 0.37 (0.17), residues: 816 loop : -0.62 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.019 0.001 TYR B1067 PHE 0.024 0.001 PHE B 392 TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27670) covalent geometry : angle 0.57363 / 0.29 (37625) SS BOND : bond 0.00349 / 0.21 ( 42) SS BOND : angle 2.05966 / 1.41 ( 84) hydrogen bonds : bond 0.04096 / 2.62 ( 1128) hydrogen bonds : angle 5.37619 / 3.79 ( 3021) link_BETA1-4 : bond 0.00218 / 0.14 ( 20) link_BETA1-4 : angle 1.11812 / 0.75 ( 60) link_NAG-ASN : bond 0.00202 / 0.14 ( 42) link_NAG-ASN : angle 1.67950 / 1.17 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7649 (ptt180) cc_final: 0.7226 (mtm180) REVERT: A 347 PHE cc_start: 0.6478 (m-80) cc_final: 0.5948 (m-10) REVERT: A 428 ASP cc_start: 0.7645 (p0) cc_final: 0.7032 (t0) REVERT: A 955 ASN cc_start: 0.9044 (m-40) cc_final: 0.8713 (t0) REVERT: B 118 LEU cc_start: 0.8630 (tt) cc_final: 0.8263 (mt) REVERT: B 223 LEU cc_start: 0.8948 (mp) cc_final: 0.8745 (mt) REVERT: B 508 TYR cc_start: 0.7454 (m-80) cc_final: 0.7192 (m-80) REVERT: B 515 PHE cc_start: 0.8353 (m-10) cc_final: 0.8149 (m-80) REVERT: B 549 THR cc_start: 0.9090 (m) cc_final: 0.8775 (p) REVERT: B 558 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7617 (mttt) REVERT: C 699 LEU cc_start: 0.7928 (mt) cc_final: 0.7625 (mp) REVERT: C 901 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8798 (tp-100) REVERT: Y 12 MET cc_start: 0.4507 (tpt) cc_final: 0.4261 (mmm) REVERT: Y 34 MET cc_start: 0.7340 (tpp) cc_final: 0.6449 (mtm) REVERT: Y 74 LYS cc_start: 0.6800 (ptmm) cc_final: 0.6564 (ttpp) REVERT: Y 80 TYR cc_start: 0.6951 (m-80) cc_final: 0.6689 (m-10) REVERT: Z 34 MET cc_start: 0.1761 (mmp) cc_final: 0.0829 (ppp) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1569 time to fit residues: 68.5367 Evaluate side-chains 159 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 136 optimal weight: 0.9990 chunk 311 optimal weight: 30.0000 chunk 229 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 235 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 935 GLN A 957 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Y 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096786 restraints weight = 63039.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094427 restraints weight = 72383.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094828 restraints weight = 66898.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095340 restraints weight = 56749.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096116 restraints weight = 44526.414| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27774 Z= 0.177 Angle : 0.630 11.826 37895 Z= 0.318 Chirality : 0.046 0.250 4437 Planarity : 0.004 0.065 4766 Dihedral : 4.555 34.430 3600 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.00 (0.14), residues: 3289 helix: 1.43 (0.21), residues: 645 sheet: 0.33 (0.17), residues: 819 loop : -0.66 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.020 0.001 TYR A 904 PHE 0.031 0.002 PHE A 497 TRP 0.014 0.001 TRP Y 36 HIS 0.008 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (27670) covalent geometry : angle 0.61401 / 0.31 (37625) SS BOND : bond 0.00287 / 0.19 ( 42) SS BOND : angle 2.07905 / 1.43 ( 84) hydrogen bonds : bond 0.04335 / 2.79 ( 1128) hydrogen bonds : angle 5.42464 / 3.82 ( 3021) link_BETA1-4 : bond 0.00245 / 0.16 ( 20) link_BETA1-4 : angle 1.20090 / 0.80 ( 60) link_NAG-ASN : bond 0.00266 / 0.18 ( 42) link_NAG-ASN : angle 1.76918 / 1.22 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7760 (ptt180) cc_final: 0.7283 (mtm180) REVERT: A 347 PHE cc_start: 0.6668 (m-80) cc_final: 0.6138 (m-10) REVERT: A 369 TYR cc_start: 0.8149 (t80) cc_final: 0.7813 (t80) REVERT: A 428 ASP cc_start: 0.7610 (p0) cc_final: 0.7051 (t0) REVERT: A 896 ILE cc_start: 0.9430 (tt) cc_final: 0.9158 (pt) REVERT: A 955 ASN cc_start: 0.9043 (m-40) cc_final: 0.8749 (t0) REVERT: B 54 LEU cc_start: 0.8045 (mm) cc_final: 0.7516 (tp) REVERT: B 118 LEU cc_start: 0.8628 (tt) cc_final: 0.8192 (mt) REVERT: B 239 GLN cc_start: 0.5205 (tp40) cc_final: 0.4958 (tp40) REVERT: B 465 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 549 THR cc_start: 0.9100 (m) cc_final: 0.8818 (p) REVERT: B 558 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7684 (mtpt) REVERT: C 324 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7473 (mp0) REVERT: C 618 THR cc_start: 0.8689 (p) cc_final: 0.8408 (t) REVERT: Y 34 MET cc_start: 0.7447 (tpp) cc_final: 0.6483 (mtm) REVERT: Y 80 TYR cc_start: 0.6930 (m-80) cc_final: 0.6720 (m-10) REVERT: Z 34 MET cc_start: 0.1178 (mmp) cc_final: 0.0620 (tmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1510 time to fit residues: 61.8259 Evaluate side-chains 161 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 199 optimal weight: 0.0970 chunk 287 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 123 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 913 GLN A 957 GLN B 125 ASN B 901 GLN B 992 GLN C 87 ASN C 493 GLN C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098250 restraints weight = 61610.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097592 restraints weight = 57234.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098272 restraints weight = 45260.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098623 restraints weight = 37820.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098924 restraints weight = 33516.570| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 27774 Z= 0.112 Angle : 0.579 10.992 37895 Z= 0.293 Chirality : 0.044 0.243 4437 Planarity : 0.004 0.067 4766 Dihedral : 4.362 32.751 3600 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3289 helix: 1.61 (0.21), residues: 651 sheet: 0.43 (0.17), residues: 831 loop : -0.59 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 19 TYR 0.019 0.001 TYR B 369 PHE 0.029 0.001 PHE B 392 TRP 0.015 0.001 TRP Y 36 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (27670) covalent geometry : angle 0.56407 / 0.29 (37625) SS BOND : bond 0.00360 / 0.26 ( 42) SS BOND : angle 1.90776 / 1.28 ( 84) hydrogen bonds : bond 0.03931 / 2.53 ( 1128) hydrogen bonds : angle 5.29318 / 3.74 ( 3021) link_BETA1-4 : bond 0.00400 / 0.26 ( 20) link_BETA1-4 : angle 1.07904 / 0.74 ( 60) link_NAG-ASN : bond 0.00173 / 0.11 ( 42) link_NAG-ASN : angle 1.64999 / 1.12 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7779 (ptt180) cc_final: 0.7347 (mtm180) REVERT: A 428 ASP cc_start: 0.7689 (p0) cc_final: 0.7086 (t0) REVERT: A 540 ASN cc_start: 0.7801 (t0) cc_final: 0.7536 (t0) REVERT: A 896 ILE cc_start: 0.9381 (tt) cc_final: 0.9127 (pt) REVERT: A 955 ASN cc_start: 0.8993 (m-40) cc_final: 0.8735 (t0) REVERT: B 54 LEU cc_start: 0.7927 (mm) cc_final: 0.7465 (tp) REVERT: B 118 LEU cc_start: 0.8590 (tt) cc_final: 0.8163 (mt) REVERT: B 239 GLN cc_start: 0.5193 (tp40) cc_final: 0.4740 (tp40) REVERT: B 420 ASP cc_start: 0.7080 (m-30) cc_final: 0.6850 (m-30) REVERT: B 465 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 515 PHE cc_start: 0.8472 (m-10) cc_final: 0.8228 (m-80) REVERT: B 549 THR cc_start: 0.9012 (m) cc_final: 0.8755 (p) REVERT: B 558 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7553 (mtpt) REVERT: C 324 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7521 (mp0) REVERT: C 618 THR cc_start: 0.8560 (p) cc_final: 0.8212 (t) REVERT: Y 34 MET cc_start: 0.7353 (tpp) cc_final: 0.6513 (mtm) REVERT: Y 80 TYR cc_start: 0.6811 (m-80) cc_final: 0.6600 (m-10) REVERT: Z 12 MET cc_start: -0.2216 (mtt) cc_final: -0.2569 (ptp) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.1459 time to fit residues: 64.2791 Evaluate side-chains 164 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 156 optimal weight: 0.0020 chunk 56 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 325 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 957 GLN C 784 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093967 restraints weight = 62474.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093465 restraints weight = 53029.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093795 restraints weight = 40180.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094419 restraints weight = 34108.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094622 restraints weight = 29567.117| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27774 Z= 0.109 Angle : 0.560 10.587 37895 Z= 0.284 Chirality : 0.044 0.247 4437 Planarity : 0.004 0.067 4766 Dihedral : 4.215 28.022 3600 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3289 helix: 1.77 (0.21), residues: 645 sheet: 0.49 (0.17), residues: 832 loop : -0.51 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.018 0.001 TYR B1067 PHE 0.017 0.001 PHE Y 68 TRP 0.022 0.001 TRP Y 36 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (27670) covalent geometry : angle 0.54751 / 0.28 (37625) SS BOND : bond 0.00500 / 0.21 ( 42) SS BOND : angle 1.67604 / 1.13 ( 84) hydrogen bonds : bond 0.03805 / 2.44 ( 1128) hydrogen bonds : angle 5.19207 / 3.68 ( 3021) link_BETA1-4 : bond 0.00257 / 0.16 ( 20) link_BETA1-4 : angle 1.08176 / 0.74 ( 60) link_NAG-ASN : bond 0.00144 / 0.10 ( 42) link_NAG-ASN : angle 1.56033 / 1.07 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7733 (ptt180) cc_final: 0.7346 (mtm180) REVERT: A 347 PHE cc_start: 0.6470 (m-80) cc_final: 0.5621 (m-10) REVERT: A 428 ASP cc_start: 0.7641 (p0) cc_final: 0.7006 (t0) REVERT: A 495 TYR cc_start: 0.5158 (m-80) cc_final: 0.4826 (m-80) REVERT: A 540 ASN cc_start: 0.7768 (t0) cc_final: 0.7504 (t0) REVERT: A 955 ASN cc_start: 0.8986 (m-40) cc_final: 0.8779 (t0) REVERT: B 54 LEU cc_start: 0.7892 (mm) cc_final: 0.7505 (tp) REVERT: B 118 LEU cc_start: 0.8638 (tt) cc_final: 0.8246 (mt) REVERT: B 239 GLN cc_start: 0.5019 (tp40) cc_final: 0.4692 (tp40) REVERT: B 385 THR cc_start: 0.7854 (p) cc_final: 0.7502 (t) REVERT: B 420 ASP cc_start: 0.7191 (m-30) cc_final: 0.6898 (m-30) REVERT: B 465 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 508 TYR cc_start: 0.7606 (m-80) cc_final: 0.7365 (m-80) REVERT: B 549 THR cc_start: 0.8941 (m) cc_final: 0.8716 (p) REVERT: B 558 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7538 (mtpt) REVERT: C 313 TYR cc_start: 0.8896 (m-80) cc_final: 0.8585 (m-80) REVERT: C 324 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7500 (mp0) REVERT: Y 12 MET cc_start: 0.4615 (tpt) cc_final: 0.4353 (mmm) REVERT: Y 34 MET cc_start: 0.7314 (tpp) cc_final: 0.6523 (mtm) REVERT: Z 12 MET cc_start: -0.1945 (mtt) cc_final: -0.2344 (ptp) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1420 time to fit residues: 63.1900 Evaluate side-chains 167 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 935 GLN A 957 GLN B 992 GLN C 321 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099058 restraints weight = 61224.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098231 restraints weight = 55488.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099334 restraints weight = 42917.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099546 restraints weight = 35624.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099732 restraints weight = 31695.782| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27774 Z= 0.112 Angle : 0.560 11.284 37895 Z= 0.284 Chirality : 0.044 0.249 4437 Planarity : 0.004 0.066 4766 Dihedral : 4.169 28.116 3600 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3289 helix: 1.81 (0.21), residues: 644 sheet: 0.51 (0.17), residues: 823 loop : -0.51 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.024 0.001 TYR A 369 PHE 0.025 0.001 PHE A 55 TRP 0.019 0.001 TRP Y 36 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (27670) covalent geometry : angle 0.54746 / 0.28 (37625) SS BOND : bond 0.00296 / 0.17 ( 42) SS BOND : angle 1.65995 / 1.11 ( 84) hydrogen bonds : bond 0.03769 / 2.42 ( 1128) hydrogen bonds : angle 5.14636 / 3.64 ( 3021) link_BETA1-4 : bond 0.00276 / 0.17 ( 20) link_BETA1-4 : angle 1.09401 / 0.75 ( 60) link_NAG-ASN : bond 0.00150 / 0.10 ( 42) link_NAG-ASN : angle 1.52214 / 1.05 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3654.33 seconds wall clock time: 64 minutes 28.75 seconds (3868.75 seconds total)