Starting phenix.real_space_refine on Mon Sep 14 01:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zp2_11334/09_2026/6zp2_11334.map" } resolution = 3.1 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= 0.007 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 17106 2.51 5 N 4380 2.21 5 O 5265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 201 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8572 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1044} Chain breaks: 4 Chain: "B" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8572 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1044} Chain breaks: 4 Chain: "C" Number of atoms: 8572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8572 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1044} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 265 Unusual residues: {'BLA': 1, 'EIC': 2, 'NAG': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.10, per 1000 atoms: 0.23 Number of scatterers: 26871 At special positions: 0 Unit cell: (142.174, 151.723, 169.76, 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 5265 8.00 N 4380 7.00 C 17106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.99 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.99 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.99 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A2102 " - " ASN A 331 " " NAG A2103 " - " ASN A 603 " " NAG A2104 " - " ASN A 616 " " NAG A2105 " - " ASN A 657 " " NAG A2106 " - " ASN A 709 " " NAG A2107 " - " ASN A1074 " " NAG A2108 " - " ASN A1098 " " NAG A2110 " - " ASN A 282 " " NAG A2111 " - " ASN A 343 " " NAG A2113 " - " ASN A 17 " " NAG A2114 " - " ASN A 61 " " NAG A2115 " - " ASN A 149 " " NAG B2102 " - " ASN B 331 " " NAG B2103 " - " ASN B 603 " " NAG B2104 " - " ASN B 616 " " NAG B2105 " - " ASN B 657 " " NAG B2106 " - " ASN B 709 " " NAG B2107 " - " ASN B1074 " " NAG B2108 " - " ASN B1098 " " NAG B2110 " - " ASN B 282 " " NAG B2111 " - " ASN B 343 " " NAG B2113 " - " ASN B 17 " " NAG B2114 " - " ASN B 61 " " NAG B2115 " - " ASN B 149 " " NAG C2102 " - " ASN C 331 " " NAG C2103 " - " ASN C 603 " " NAG C2104 " - " ASN C 616 " " NAG C2105 " - " ASN C 657 " " NAG C2106 " - " ASN C 709 " " NAG C2107 " - " ASN C1074 " " NAG C2108 " - " ASN C1098 " " NAG C2110 " - " ASN C 282 " " NAG C2111 " - " ASN C 343 " " NAG C2112 " - " ASN C 17 " " NAG C2113 " - " ASN C 61 " " NAG C2114 " - " ASN C 149 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 122 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 122 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 24.8% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.871A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.177A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.700A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.709A 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: 4.238A 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: 4.066A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.571A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.871A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.177A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.700A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.709A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.239A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.066A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.572A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.872A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.176A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.250A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.700A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.708A 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: 4.238A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.066A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.572A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.724A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.724A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.937A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.308A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.686A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.280A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.726A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.726A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.425A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.931A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.487A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.487A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.782A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.725A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.725A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.937A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.308A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.686A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.279A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.727A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.727A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.424A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.487A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.487A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.783A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.724A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.937A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.307A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.752A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.279A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.726A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.726A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.424A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.487A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.487A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.459A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.782A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1211 hydrogen bonds defined for protein. 3345 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: 7.25 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4351 1.31 - 1.45: 8072 1.45 - 1.58: 14901 1.58 - 1.72: 6 1.72 - 1.86: 144 Bond restraints: 27474 Sorted by residual: bond pdb=" C1C BLA A2101 " pdb=" NC BLA A2101 " ideal model delta sigma weight residual 1.368 1.528 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" C1C BLA B2101 " pdb=" NC BLA B2101 " ideal model delta sigma weight residual 1.368 1.527 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C1C BLA C2101 " pdb=" NC BLA C2101 " ideal model delta sigma weight residual 1.368 1.526 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C4C BLA C2101 " pdb=" NC BLA C2101 " ideal model delta sigma weight residual 1.375 1.533 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C4C BLA B2101 " pdb=" NC BLA B2101 " ideal model delta sigma weight residual 1.375 1.532 -0.157 2.00e-02 2.50e+03 6.19e+01 ... (remaining 27469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.99: 37198 6.99 - 13.97: 161 13.97 - 20.96: 6 20.96 - 27.94: 9 27.94 - 34.93: 3 Bond angle restraints: 37377 Sorted by residual: angle pdb=" CB MET B 902 " pdb=" CG MET B 902 " pdb=" SD MET B 902 " ideal model delta sigma weight residual 112.70 147.63 -34.93 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CB MET C 902 " pdb=" CG MET C 902 " pdb=" SD MET C 902 " ideal model delta sigma weight residual 112.70 147.61 -34.91 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CB MET A 902 " pdb=" CG MET A 902 " pdb=" SD MET A 902 " ideal model delta sigma weight residual 112.70 147.59 -34.89 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG ARG A 273 " pdb=" CD ARG A 273 " pdb=" NE ARG A 273 " ideal model delta sigma weight residual 112.00 136.46 -24.46 2.20e+00 2.07e-01 1.24e+02 angle pdb=" CG ARG C 273 " pdb=" CD ARG C 273 " pdb=" NE ARG C 273 " ideal model delta sigma weight residual 112.00 136.46 -24.46 2.20e+00 2.07e-01 1.24e+02 ... (remaining 37372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14666 17.98 - 35.97: 790 35.97 - 53.95: 216 53.95 - 71.94: 66 71.94 - 89.92: 18 Dihedral angle restraints: 15756 sinusoidal: 6183 harmonic: 9573 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.37 -60.63 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.45 -60.55 1 1.00e+01 1.00e-02 4.88e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.45 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 15753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4073 0.137 - 0.274: 268 0.274 - 0.412: 30 0.412 - 0.549: 6 0.549 - 0.686: 12 Chirality restraints: 4389 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 -2.55 0.15 2.00e-02 2.50e+03 5.61e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.49e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.43e+01 ... (remaining 4386 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A2101 " -0.013 2.00e-02 2.50e+03 8.40e-02 1.76e+02 pdb=" C1D BLA A2101 " 0.191 2.00e-02 2.50e+03 pdb=" C2C BLA A2101 " 0.011 2.00e-02 2.50e+03 pdb=" C3C BLA A2101 " -0.000 2.00e-02 2.50e+03 pdb=" C4C BLA A2101 " -0.078 2.00e-02 2.50e+03 pdb=" CAC BLA A2101 " -0.009 2.00e-02 2.50e+03 pdb=" CHD BLA A2101 " -0.115 2.00e-02 2.50e+03 pdb=" CMC BLA A2101 " 0.094 2.00e-02 2.50e+03 pdb=" NC BLA A2101 " -0.077 2.00e-02 2.50e+03 pdb=" OC BLA A2101 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B2101 " -0.013 2.00e-02 2.50e+03 8.39e-02 1.76e+02 pdb=" C1D BLA B2101 " 0.191 2.00e-02 2.50e+03 pdb=" C2C BLA B2101 " 0.012 2.00e-02 2.50e+03 pdb=" C3C BLA B2101 " -0.001 2.00e-02 2.50e+03 pdb=" C4C BLA B2101 " -0.077 2.00e-02 2.50e+03 pdb=" CAC BLA B2101 " -0.009 2.00e-02 2.50e+03 pdb=" CHD BLA B2101 " -0.115 2.00e-02 2.50e+03 pdb=" CMC BLA B2101 " 0.093 2.00e-02 2.50e+03 pdb=" NC BLA B2101 " -0.077 2.00e-02 2.50e+03 pdb=" OC BLA B2101 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA C2101 " 0.013 2.00e-02 2.50e+03 8.37e-02 1.75e+02 pdb=" C1D BLA C2101 " -0.190 2.00e-02 2.50e+03 pdb=" C2C BLA C2101 " -0.012 2.00e-02 2.50e+03 pdb=" C3C BLA C2101 " 0.001 2.00e-02 2.50e+03 pdb=" C4C BLA C2101 " 0.077 2.00e-02 2.50e+03 pdb=" CAC BLA C2101 " 0.009 2.00e-02 2.50e+03 pdb=" CHD BLA C2101 " 0.114 2.00e-02 2.50e+03 pdb=" CMC BLA C2101 " -0.093 2.00e-02 2.50e+03 pdb=" NC BLA C2101 " 0.077 2.00e-02 2.50e+03 pdb=" OC BLA C2101 " 0.004 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3372 2.74 - 3.28: 25767 3.28 - 3.82: 43681 3.82 - 4.36: 54967 4.36 - 4.90: 93101 Nonbonded interactions: 220888 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.205 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OG SER B 813 " model vdw 2.205 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OG SER C 813 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.256 3.040 ... (remaining 220883 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 14 through 2111 or resid 2113 through 2114)) selection = (chain 'B' and (resid 14 through 2111 or resid 2113 through 2114)) selection = (chain 'C' and (resid 14 through 2111 or resid 2113 through 2114)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 27.540 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.014 0.518 27585 Z= 0.676 Angle : 1.618 34.927 37665 Z= 0.876 Chirality : 0.085 0.686 4389 Planarity : 0.009 0.084 4746 Dihedral : 12.964 89.920 9471 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 1.05 % Allowed : 1.36 % Favored : 97.59 % Cbeta Deviations : 0.29 % 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: -0.00 (0.13), residues: 3261 helix: 0.28 (0.18), residues: 705 sheet: 0.91 (0.18), residues: 672 loop : -0.41 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.003 ARG C1091 TYR 0.071 0.003 TYR B 904 PHE 0.087 0.006 PHE A 220 TRP 0.026 0.003 TRP C 104 HIS 0.045 0.004 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.01066 / 0.49 (27474) covalent geometry : angle 1.56363 / 0.86 (37377) SS BOND : bond 0.01629 / 0.86 ( 45) SS BOND : angle 4.19339 / 2.96 ( 90) hydrogen bonds : bond 0.13575 / 8.79 ( 1073) hydrogen bonds : angle 7.88063 / 5.47 ( 3345) link_BETA1-4 : bond 0.00522 / 0.32 ( 15) link_BETA1-4 : angle 2.51038 / 1.64 ( 45) link_NAG-ASN : bond 0.21616 / 11.21 ( 51) link_NAG-ASN : angle 5.88954 / 4.58 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 1073 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: B 153 MET cc_start: 0.6665 (ptt) cc_final: 0.6368 (ptt) REVERT: B 1073 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8115 (mmtp) REVERT: C 220 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7193 (t80) REVERT: C 697 MET cc_start: 0.8402 (ptm) cc_final: 0.8138 (ptm) REVERT: C 985 ASP cc_start: 0.7847 (p0) cc_final: 0.7588 (p0) outliers start: 30 outliers final: 1 residues processed: 286 average time/residue: 0.1919 time to fit residues: 86.8350 Evaluate side-chains 194 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 220 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1119 ASN B 23 GLN B 165 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1119 ASN C 165 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090703 restraints weight = 45812.870| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.16 r_work: 0.3002 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27585 Z= 0.147 Angle : 0.660 12.278 37665 Z= 0.338 Chirality : 0.049 0.495 4389 Planarity : 0.004 0.044 4746 Dihedral : 6.676 62.265 3627 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.63 % Allowed : 4.30 % Favored : 95.07 % 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: 0.48 (0.14), residues: 3261 helix: 1.26 (0.19), residues: 708 sheet: 0.99 (0.18), residues: 675 loop : -0.26 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 273 TYR 0.026 0.001 TYR A 904 PHE 0.023 0.002 PHE B 392 TRP 0.017 0.001 TRP A 152 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (27474) covalent geometry : angle 0.61907 / 0.33 (37377) SS BOND : bond 0.00409 / 0.27 ( 45) SS BOND : angle 1.70064 / 1.27 ( 90) hydrogen bonds : bond 0.04910 / 3.24 ( 1073) hydrogen bonds : angle 6.05925 / 4.22 ( 3345) link_BETA1-4 : bond 0.00409 / 0.24 ( 15) link_BETA1-4 : angle 1.78444 / 1.11 ( 45) link_NAG-ASN : bond 0.00756 / 0.47 ( 51) link_NAG-ASN : angle 3.28754 / 2.31 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7142 (ptt) cc_final: 0.6683 (ptt) REVERT: A 291 CYS cc_start: 0.6717 (t) cc_final: 0.6509 (m) REVERT: A 1073 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8434 (mttm) REVERT: A 1110 TYR cc_start: 0.8660 (t80) cc_final: 0.8327 (t80) REVERT: A 1111 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: B 153 MET cc_start: 0.7156 (ptt) cc_final: 0.6793 (ptt) REVERT: B 1110 TYR cc_start: 0.8686 (t80) cc_final: 0.8486 (t80) REVERT: C 140 PHE cc_start: 0.8906 (p90) cc_final: 0.8542 (p90) REVERT: C 153 MET cc_start: 0.7110 (ptt) cc_final: 0.6790 (ptt) REVERT: C 346 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7814 (mmm-85) outliers start: 18 outliers final: 10 residues processed: 230 average time/residue: 0.1839 time to fit residues: 68.1631 Evaluate side-chains 187 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 658 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 204 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 108 optimal weight: 0.0980 chunk 220 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 296 optimal weight: 0.5980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085374 restraints weight = 45912.287| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.96 r_work: 0.2922 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27585 Z= 0.152 Angle : 0.583 12.664 37665 Z= 0.296 Chirality : 0.047 0.445 4389 Planarity : 0.004 0.043 4746 Dihedral : 6.240 62.726 3619 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.73 % Allowed : 5.63 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3261 helix: 1.34 (0.20), residues: 726 sheet: 0.87 (0.18), residues: 699 loop : -0.29 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 646 TYR 0.040 0.001 TYR A 904 PHE 0.018 0.002 PHE C 329 TRP 0.013 0.001 TRP B 258 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (27474) covalent geometry : angle 0.54447 / 0.29 (37377) SS BOND : bond 0.00469 / 0.31 ( 45) SS BOND : angle 1.95849 / 1.50 ( 90) hydrogen bonds : bond 0.04178 / 2.78 ( 1073) hydrogen bonds : angle 5.53815 / 3.85 ( 3345) link_BETA1-4 : bond 0.00468 / 0.27 ( 15) link_BETA1-4 : angle 1.46986 / 0.94 ( 45) link_NAG-ASN : bond 0.00681 / 0.42 ( 51) link_NAG-ASN : angle 2.89092 / 1.85 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 1.054 Fit side-chains REVERT: A 228 ASP cc_start: 0.7080 (p0) cc_final: 0.6715 (p0) REVERT: A 902 MET cc_start: 0.8982 (tpp) cc_final: 0.8589 (mmt) REVERT: A 1110 TYR cc_start: 0.8731 (t80) cc_final: 0.8508 (t80) REVERT: A 1117 THR cc_start: 0.8943 (m) cc_final: 0.8702 (p) REVERT: B 153 MET cc_start: 0.7056 (ptt) cc_final: 0.6718 (ptt) REVERT: B 378 LYS cc_start: 0.8931 (tttp) cc_final: 0.8645 (ttmt) REVERT: B 955 ASN cc_start: 0.8444 (m110) cc_final: 0.8222 (m110) REVERT: B 1110 TYR cc_start: 0.8761 (t80) cc_final: 0.8546 (t80) REVERT: C 153 MET cc_start: 0.7347 (ptt) cc_final: 0.6962 (ptt) REVERT: C 200 TYR cc_start: 0.8837 (m-80) cc_final: 0.8631 (m-80) outliers start: 21 outliers final: 15 residues processed: 223 average time/residue: 0.1782 time to fit residues: 64.9499 Evaluate side-chains 194 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 227 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 253 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 290 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 856 ASN B 954 GLN B 957 GLN B1135 ASN C 52 GLN C 422 ASN C 856 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.078537 restraints weight = 46123.795| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.93 r_work: 0.2821 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 27585 Z= 0.251 Angle : 0.634 11.686 37665 Z= 0.322 Chirality : 0.049 0.448 4389 Planarity : 0.004 0.047 4746 Dihedral : 6.193 61.994 3615 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.50 % Allowed : 6.95 % Favored : 91.54 % 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: 3261 helix: 1.07 (0.19), residues: 729 sheet: 0.65 (0.18), residues: 747 loop : -0.33 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.049 0.002 TYR B 904 PHE 0.021 0.002 PHE C 329 TRP 0.019 0.001 TRP A 152 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (27474) covalent geometry : angle 0.60178 / 0.31 (37377) SS BOND : bond 0.00609 / 0.41 ( 45) SS BOND : angle 1.91047 / 1.45 ( 90) hydrogen bonds : bond 0.04700 / 3.11 ( 1073) hydrogen bonds : angle 5.67793 / 3.95 ( 3345) link_BETA1-4 : bond 0.00432 / 0.26 ( 15) link_BETA1-4 : angle 1.46891 / 0.95 ( 45) link_NAG-ASN : bond 0.00633 / 0.39 ( 51) link_NAG-ASN : angle 2.78352 / 1.80 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6721 (ptt) REVERT: A 228 ASP cc_start: 0.7279 (p0) cc_final: 0.6909 (p0) REVERT: A 291 CYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6888 (m) REVERT: A 764 ASN cc_start: 0.9036 (m-40) cc_final: 0.8794 (m-40) REVERT: A 1107 ARG cc_start: 0.8384 (mtt90) cc_final: 0.8138 (mtt90) REVERT: A 1117 THR cc_start: 0.9137 (m) cc_final: 0.8931 (p) REVERT: B 65 PHE cc_start: 0.8900 (m-80) cc_final: 0.8566 (m-80) REVERT: B 111 ASP cc_start: 0.7447 (p0) cc_final: 0.7164 (p0) REVERT: B 153 MET cc_start: 0.7135 (ptt) cc_final: 0.6816 (ptt) REVERT: B 378 LYS cc_start: 0.9028 (tttp) cc_final: 0.8666 (ttmm) REVERT: B 955 ASN cc_start: 0.8604 (m110) cc_final: 0.8384 (m110) REVERT: B 988 GLU cc_start: 0.8674 (mp0) cc_final: 0.8301 (mp0) REVERT: C 153 MET cc_start: 0.7491 (ptt) cc_final: 0.7222 (ptt) REVERT: C 200 TYR cc_start: 0.8885 (m-80) cc_final: 0.8580 (m-80) REVERT: C 228 ASP cc_start: 0.7224 (p0) cc_final: 0.6793 (p0) REVERT: C 904 TYR cc_start: 0.8121 (m-80) cc_final: 0.7889 (m-80) REVERT: C 1117 THR cc_start: 0.9089 (m) cc_final: 0.8879 (p) outliers start: 43 outliers final: 24 residues processed: 225 average time/residue: 0.1731 time to fit residues: 64.2575 Evaluate side-chains 197 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 276 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 317 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 422 ASN A1135 ASN B 52 GLN B 196 ASN B 422 ASN C 52 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.082254 restraints weight = 46035.311| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.92 r_work: 0.2871 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27585 Z= 0.118 Angle : 0.541 11.334 37665 Z= 0.273 Chirality : 0.046 0.443 4389 Planarity : 0.004 0.043 4746 Dihedral : 5.762 62.677 3615 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.05 % Allowed : 8.18 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3261 helix: 1.30 (0.20), residues: 729 sheet: 0.74 (0.18), residues: 699 loop : -0.29 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.023 0.001 TYR A 904 PHE 0.015 0.001 PHE B 157 TRP 0.012 0.001 TRP A 152 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (27474) covalent geometry : angle 0.51001 / 0.27 (37377) SS BOND : bond 0.00322 / 0.21 ( 45) SS BOND : angle 1.42071 / 1.11 ( 90) hydrogen bonds : bond 0.03998 / 2.64 ( 1073) hydrogen bonds : angle 5.41156 / 3.77 ( 3345) link_BETA1-4 : bond 0.00392 / 0.24 ( 15) link_BETA1-4 : angle 1.40942 / 0.91 ( 45) link_NAG-ASN : bond 0.00640 / 0.40 ( 51) link_NAG-ASN : angle 2.61070 / 1.67 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7071 (ptt) cc_final: 0.6832 (ptt) REVERT: A 228 ASP cc_start: 0.7124 (p0) cc_final: 0.6875 (p0) REVERT: A 902 MET cc_start: 0.9081 (tpp) cc_final: 0.8814 (tpp) REVERT: A 985 ASP cc_start: 0.8347 (p0) cc_final: 0.7605 (p0) REVERT: A 1117 THR cc_start: 0.9137 (m) cc_final: 0.8929 (p) REVERT: B 65 PHE cc_start: 0.8838 (m-80) cc_final: 0.8530 (m-80) REVERT: B 111 ASP cc_start: 0.7277 (p0) cc_final: 0.6971 (p0) REVERT: B 153 MET cc_start: 0.7113 (ptt) cc_final: 0.6792 (ptt) REVERT: B 955 ASN cc_start: 0.8565 (m110) cc_final: 0.8313 (m110) REVERT: B 988 GLU cc_start: 0.8684 (mp0) cc_final: 0.8353 (mp0) REVERT: C 153 MET cc_start: 0.7510 (ptt) cc_final: 0.7182 (ptt) REVERT: C 200 TYR cc_start: 0.8784 (m-80) cc_final: 0.8510 (m-80) REVERT: C 228 ASP cc_start: 0.7224 (p0) cc_final: 0.6795 (p0) outliers start: 30 outliers final: 15 residues processed: 229 average time/residue: 0.1776 time to fit residues: 66.9805 Evaluate side-chains 191 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 304 optimal weight: 5.9990 chunk 222 optimal weight: 0.0870 chunk 26 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 764 ASN C 52 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.078040 restraints weight = 46563.425| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.91 r_work: 0.2794 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 27585 Z= 0.281 Angle : 0.635 11.125 37665 Z= 0.322 Chirality : 0.048 0.435 4389 Planarity : 0.004 0.046 4746 Dihedral : 5.901 62.523 3615 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.26 % Allowed : 8.18 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3261 helix: 1.17 (0.20), residues: 726 sheet: 0.50 (0.17), residues: 765 loop : -0.39 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1107 TYR 0.041 0.002 TYR B 904 PHE 0.017 0.002 PHE C 133 TRP 0.010 0.001 TRP A 152 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.28 (27474) covalent geometry : angle 0.59886 / 0.31 (37377) SS BOND : bond 0.00626 / 0.42 ( 45) SS BOND : angle 2.64642 / 2.12 ( 90) hydrogen bonds : bond 0.04652 / 3.07 ( 1073) hydrogen bonds : angle 5.62115 / 3.91 ( 3345) link_BETA1-4 : bond 0.00284 / 0.17 ( 15) link_BETA1-4 : angle 1.38998 / 0.90 ( 45) link_NAG-ASN : bond 0.00603 / 0.38 ( 51) link_NAG-ASN : angle 2.65122 / 1.71 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7134 (ptt) cc_final: 0.6881 (ptt) REVERT: A 228 ASP cc_start: 0.7274 (p0) cc_final: 0.7031 (p0) REVERT: A 902 MET cc_start: 0.9136 (tpp) cc_final: 0.8826 (tpp) REVERT: B 65 PHE cc_start: 0.8924 (m-80) cc_final: 0.8528 (m-80) REVERT: B 111 ASP cc_start: 0.7590 (p0) cc_final: 0.7321 (p0) REVERT: B 153 MET cc_start: 0.7059 (ptt) cc_final: 0.6717 (ptt) REVERT: B 228 ASP cc_start: 0.7494 (p0) cc_final: 0.7234 (p0) REVERT: B 568 ASP cc_start: 0.8030 (m-30) cc_final: 0.7822 (m-30) REVERT: B 985 ASP cc_start: 0.8132 (p0) cc_final: 0.7788 (p0) REVERT: C 111 ASP cc_start: 0.7547 (p0) cc_final: 0.7226 (p0) REVERT: C 153 MET cc_start: 0.7414 (ptt) cc_final: 0.7058 (ptt) REVERT: C 200 TYR cc_start: 0.8884 (m-80) cc_final: 0.8566 (m-80) REVERT: C 212 LEU cc_start: 0.8700 (tt) cc_final: 0.8439 (tt) REVERT: C 228 ASP cc_start: 0.7407 (p0) cc_final: 0.6991 (p0) REVERT: C 568 ASP cc_start: 0.8012 (m-30) cc_final: 0.7785 (m-30) outliers start: 36 outliers final: 26 residues processed: 217 average time/residue: 0.1759 time to fit residues: 62.8347 Evaluate side-chains 197 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 422 ASN A 895 GLN B 422 ASN C 52 GLN C 314 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.081072 restraints weight = 45911.099| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.91 r_work: 0.2852 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27585 Z= 0.133 Angle : 0.548 10.757 37665 Z= 0.278 Chirality : 0.046 0.421 4389 Planarity : 0.004 0.048 4746 Dihedral : 5.495 63.126 3615 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.19 % Allowed : 9.22 % Favored : 89.59 % 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: 0.38 (0.14), residues: 3261 helix: 1.39 (0.20), residues: 729 sheet: 0.56 (0.18), residues: 765 loop : -0.33 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 646 TYR 0.025 0.001 TYR B 904 PHE 0.015 0.001 PHE B 157 TRP 0.013 0.001 TRP A 152 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (27474) covalent geometry : angle 0.51517 / 0.27 (37377) SS BOND : bond 0.00355 / 0.24 ( 45) SS BOND : angle 1.94724 / 1.54 ( 90) hydrogen bonds : bond 0.03955 / 2.60 ( 1073) hydrogen bonds : angle 5.36482 / 3.73 ( 3345) link_BETA1-4 : bond 0.00379 / 0.22 ( 15) link_BETA1-4 : angle 1.37339 / 0.89 ( 45) link_NAG-ASN : bond 0.00623 / 0.38 ( 51) link_NAG-ASN : angle 2.50080 / 1.59 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7163 (ptt) cc_final: 0.6886 (ptt) REVERT: A 212 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 228 ASP cc_start: 0.7106 (p0) cc_final: 0.6864 (p0) REVERT: A 902 MET cc_start: 0.9156 (tpp) cc_final: 0.8735 (mmt) REVERT: B 65 PHE cc_start: 0.8841 (m-80) cc_final: 0.8510 (m-80) REVERT: B 111 ASP cc_start: 0.7522 (p0) cc_final: 0.7245 (p0) REVERT: B 153 MET cc_start: 0.7079 (ptt) cc_final: 0.6769 (ptt) REVERT: B 228 ASP cc_start: 0.7318 (p0) cc_final: 0.7077 (p0) REVERT: B 983 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8392 (mtp-110) REVERT: C 153 MET cc_start: 0.7369 (ptt) cc_final: 0.7032 (ptt) REVERT: C 200 TYR cc_start: 0.8761 (m-80) cc_final: 0.8396 (m-80) REVERT: C 212 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8368 (tt) REVERT: C 228 ASP cc_start: 0.7211 (p0) cc_final: 0.6759 (p0) outliers start: 34 outliers final: 23 residues processed: 219 average time/residue: 0.1704 time to fit residues: 61.2899 Evaluate side-chains 197 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 132 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 309 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 422 ASN A 901 GLN A 955 ASN B 422 ASN C 52 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079302 restraints weight = 46397.927| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.92 r_work: 0.2816 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27585 Z= 0.192 Angle : 0.571 10.511 37665 Z= 0.291 Chirality : 0.046 0.414 4389 Planarity : 0.004 0.050 4746 Dihedral : 5.508 63.010 3615 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.26 % Allowed : 9.68 % Favored : 89.06 % 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: 0.35 (0.14), residues: 3261 helix: 1.41 (0.20), residues: 729 sheet: 0.50 (0.18), residues: 765 loop : -0.35 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 646 TYR 0.037 0.001 TYR A 904 PHE 0.015 0.001 PHE B 157 TRP 0.012 0.001 TRP A 152 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (27474) covalent geometry : angle 0.53994 / 0.28 (37377) SS BOND : bond 0.00553 / 0.39 ( 45) SS BOND : angle 1.96244 / 1.56 ( 90) hydrogen bonds : bond 0.04222 / 2.79 ( 1073) hydrogen bonds : angle 5.41059 / 3.77 ( 3345) link_BETA1-4 : bond 0.00280 / 0.16 ( 15) link_BETA1-4 : angle 1.34351 / 0.87 ( 45) link_NAG-ASN : bond 0.00590 / 0.36 ( 51) link_NAG-ASN : angle 2.49650 / 1.59 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7173 (ptt) cc_final: 0.6768 (ptt) REVERT: A 212 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 228 ASP cc_start: 0.7237 (p0) cc_final: 0.6965 (p0) REVERT: B 65 PHE cc_start: 0.8895 (m-80) cc_final: 0.8504 (m-80) REVERT: B 111 ASP cc_start: 0.7619 (p0) cc_final: 0.7356 (p0) REVERT: B 153 MET cc_start: 0.7012 (ptt) cc_final: 0.6674 (ptt) REVERT: B 228 ASP cc_start: 0.7490 (p0) cc_final: 0.7222 (p0) REVERT: B 489 TYR cc_start: 0.8661 (m-80) cc_final: 0.8333 (m-80) REVERT: C 111 ASP cc_start: 0.7492 (p0) cc_final: 0.7120 (p0) REVERT: C 153 MET cc_start: 0.7363 (ptt) cc_final: 0.7083 (ptt) REVERT: C 200 TYR cc_start: 0.8785 (m-80) cc_final: 0.8421 (m-80) REVERT: C 212 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 228 ASP cc_start: 0.7373 (p0) cc_final: 0.6935 (p0) outliers start: 36 outliers final: 31 residues processed: 208 average time/residue: 0.1736 time to fit residues: 59.7858 Evaluate side-chains 204 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 191 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 422 ASN A 955 ASN B 422 ASN B 895 GLN C 52 GLN C 422 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.081205 restraints weight = 46094.328| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.92 r_work: 0.2851 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27585 Z= 0.122 Angle : 0.536 10.243 37665 Z= 0.274 Chirality : 0.045 0.410 4389 Planarity : 0.004 0.048 4746 Dihedral : 5.319 63.141 3615 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 10.17 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3261 helix: 1.55 (0.20), residues: 720 sheet: 0.53 (0.18), residues: 765 loop : -0.27 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 646 TYR 0.027 0.001 TYR B 904 PHE 0.015 0.001 PHE B 157 TRP 0.013 0.001 TRP A 152 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27474) covalent geometry : angle 0.50704 / 0.27 (37377) SS BOND : bond 0.00351 / 0.23 ( 45) SS BOND : angle 1.61780 / 1.27 ( 90) hydrogen bonds : bond 0.03885 / 2.57 ( 1073) hydrogen bonds : angle 5.28310 / 3.68 ( 3345) link_BETA1-4 : bond 0.00370 / 0.22 ( 15) link_BETA1-4 : angle 1.34781 / 0.88 ( 45) link_NAG-ASN : bond 0.00610 / 0.38 ( 51) link_NAG-ASN : angle 2.43008 / 1.54 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.173 Fit side-chains REVERT: A 111 ASP cc_start: 0.7667 (p0) cc_final: 0.7273 (p0) REVERT: A 153 MET cc_start: 0.7107 (ptt) cc_final: 0.6708 (ptt) REVERT: A 212 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 228 ASP cc_start: 0.7197 (p0) cc_final: 0.6951 (p0) REVERT: A 378 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8581 (tptp) REVERT: B 65 PHE cc_start: 0.8841 (m-80) cc_final: 0.8525 (m-80) REVERT: B 111 ASP cc_start: 0.7554 (p0) cc_final: 0.7286 (p0) REVERT: B 153 MET cc_start: 0.7005 (ptt) cc_final: 0.6706 (ptt) REVERT: B 228 ASP cc_start: 0.7375 (p0) cc_final: 0.7098 (p0) REVERT: B 489 TYR cc_start: 0.8681 (m-80) cc_final: 0.8386 (m-80) REVERT: C 111 ASP cc_start: 0.7357 (p0) cc_final: 0.6995 (p0) REVERT: C 153 MET cc_start: 0.7341 (ptt) cc_final: 0.7069 (ptt) REVERT: C 200 TYR cc_start: 0.8740 (m-80) cc_final: 0.8329 (m-80) REVERT: C 212 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8270 (tt) REVERT: C 228 ASP cc_start: 0.7252 (p0) cc_final: 0.6769 (p0) REVERT: C 988 GLU cc_start: 0.8746 (pm20) cc_final: 0.8483 (pm20) outliers start: 31 outliers final: 25 residues processed: 215 average time/residue: 0.1706 time to fit residues: 61.2072 Evaluate side-chains 202 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 202 optimal weight: 4.9990 chunk 319 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 187 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN B 314 GLN B 422 ASN C 52 GLN C 422 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078302 restraints weight = 46338.338| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.91 r_work: 0.2799 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27585 Z= 0.249 Angle : 0.602 10.100 37665 Z= 0.306 Chirality : 0.047 0.410 4389 Planarity : 0.004 0.049 4746 Dihedral : 5.473 62.986 3615 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.19 % Allowed : 10.27 % Favored : 88.54 % 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: 0.27 (0.14), residues: 3261 helix: 1.36 (0.20), residues: 729 sheet: 0.41 (0.17), residues: 765 loop : -0.38 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 646 TYR 0.039 0.002 TYR A 904 PHE 0.015 0.002 PHE C 592 TRP 0.011 0.001 TRP A 152 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (27474) covalent geometry : angle 0.57282 / 0.30 (37377) SS BOND : bond 0.00553 / 0.37 ( 45) SS BOND : angle 2.01154 / 1.59 ( 90) hydrogen bonds : bond 0.04420 / 2.91 ( 1073) hydrogen bonds : angle 5.45421 / 3.80 ( 3345) link_BETA1-4 : bond 0.00309 / 0.18 ( 15) link_BETA1-4 : angle 1.34967 / 0.87 ( 45) link_NAG-ASN : bond 0.00579 / 0.36 ( 51) link_NAG-ASN : angle 2.46169 / 1.57 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6522 Ramachandran restraints generated. 3261 Oldfield, 0 Emsley, 3261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.249 Fit side-chains REVERT: A 153 MET cc_start: 0.7193 (ptt) cc_final: 0.6934 (ptt) REVERT: A 212 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 228 ASP cc_start: 0.7262 (p0) cc_final: 0.6984 (p0) REVERT: B 65 PHE cc_start: 0.8892 (m-80) cc_final: 0.8518 (m-80) REVERT: B 111 ASP cc_start: 0.7650 (p0) cc_final: 0.7401 (p0) REVERT: B 153 MET cc_start: 0.7000 (ptt) cc_final: 0.6675 (ptt) REVERT: B 228 ASP cc_start: 0.7542 (p0) cc_final: 0.7265 (p0) REVERT: B 489 TYR cc_start: 0.8682 (m-80) cc_final: 0.8357 (m-80) REVERT: C 66 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6669 (p-80) REVERT: C 111 ASP cc_start: 0.7648 (p0) cc_final: 0.7302 (p0) REVERT: C 153 MET cc_start: 0.7237 (ptt) cc_final: 0.6965 (ptt) REVERT: C 200 TYR cc_start: 0.8843 (m-80) cc_final: 0.8461 (m-80) REVERT: C 212 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8324 (tt) REVERT: C 228 ASP cc_start: 0.7453 (p0) cc_final: 0.7006 (p0) outliers start: 34 outliers final: 26 residues processed: 207 average time/residue: 0.1724 time to fit residues: 59.5174 Evaluate side-chains 200 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 57 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 281 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 422 ASN A 901 GLN B 422 ASN C 52 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080626 restraints weight = 45864.283| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.91 r_work: 0.2842 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27585 Z= 0.132 Angle : 0.544 10.033 37665 Z= 0.277 Chirality : 0.046 0.402 4389 Planarity : 0.004 0.048 4746 Dihedral : 5.297 63.033 3615 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.12 % Allowed : 10.34 % Favored : 88.54 % 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: 0.39 (0.14), residues: 3261 helix: 1.53 (0.20), residues: 720 sheet: 0.43 (0.18), residues: 765 loop : -0.30 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 646 TYR 0.024 0.001 TYR B 904 PHE 0.014 0.001 PHE B 157 TRP 0.014 0.001 TRP A 152 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (27474) covalent geometry : angle 0.51543 / 0.27 (37377) SS BOND : bond 0.00379 / 0.25 ( 45) SS BOND : angle 1.65043 / 1.30 ( 90) hydrogen bonds : bond 0.03940 / 2.60 ( 1073) hydrogen bonds : angle 5.29175 / 3.69 ( 3345) link_BETA1-4 : bond 0.00371 / 0.22 ( 15) link_BETA1-4 : angle 1.33807 / 0.87 ( 45) link_NAG-ASN : bond 0.00602 / 0.37 ( 51) link_NAG-ASN : angle 2.40649 / 1.52 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5736.88 seconds wall clock time: 99 minutes 40.41 seconds (5980.41 seconds total)