Starting phenix.real_space_refine on Sun Jul 5 22:37:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.cif" model { file = "/net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a95_15270/07_2026/8a95_15270.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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 135 5.16 5 C 19600 2.51 5 N 5065 2.21 5 O 6066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30866 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8292 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1006} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8289 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 55, 'TRANS': 1006} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 8221 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 54, 'TRANS': 999} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} 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: "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: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 5.49, per 1000 atoms: 0.18 Number of scatterers: 30866 At special positions: 0 Unit cell: (160.59, 167.66, 203.01, 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 135 16.00 O 6066 8.00 N 5065 7.00 C 19600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.01 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 149 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1314 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 603 " " NAG B1315 " - " ASN B 801 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 234 " " NAG C1316 " - " ASN C 801 " " NAG G 1 " - " ASN A 61 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN C 17 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 65 sheets defined 20.4% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 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 416 through 422 Processing helix chain 'A' and resid 438 through 443 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 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.814A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.653A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.883A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.300A 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 945 through 966 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.242A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.294A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.618A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.549A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.026A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.751A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.507A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.671A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.273A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.163A 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 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 4.036A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) 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 755 removed outlier: 3.969A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.013A 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 945 through 967 removed outlier: 3.571A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.182A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'R' and resid 27 through 32 removed outlier: 3.982A pdb=" N THR R 31 " --> pdb=" O GLY R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR R 91 " --> pdb=" O TYR R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.893A pdb=" N THR S 91 " --> pdb=" O TYR S 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 removed outlier: 4.259A pdb=" N SER P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR P 33 " --> pdb=" O SER P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 33' Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.115A pdb=" N THR T 31 " --> pdb=" O GLY T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.946A pdb=" N THR T 91 " --> pdb=" O TYR T 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.942A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.376A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.878A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.903A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.664A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.580A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.546A 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: 4.452A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.029A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 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: 6.192A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.004A pdb=" N ALA A 701 " --> pdb=" O ILE B 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: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.306A 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 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.034A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.239A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.502A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.716A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.716A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.441A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.734A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.713A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.713A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (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: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.666A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.300A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.298A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 85 removed outlier: 12.707A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.711A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.740A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.481A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.870A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.977A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.353A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.353A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'R' and resid 9 through 11 removed outlier: 3.689A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN R 59 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 9 through 11 removed outlier: 3.689A pdb=" N THR R 120 " --> pdb=" O GLU R 10 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR R 112 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.577A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'O' and resid 45 through 49 removed outlier: 6.304A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 64 through 65 Processing sheet with id=AG1, first strand: chain 'S' and resid 9 through 11 removed outlier: 3.950A pdb=" N THR S 120 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE S 34 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 9 through 11 removed outlier: 3.950A pdb=" N THR S 120 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR S 112 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.538A pdb=" N VAL S 18 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 45 through 47 Processing sheet with id=AG5, first strand: chain 'P' and resid 63 through 65 Processing sheet with id=AG6, first strand: chain 'P' and resid 90 through 91 Processing sheet with id=AG7, first strand: chain 'T' and resid 10 through 11 removed outlier: 4.153A pdb=" N THR T 120 " --> pdb=" O GLU T 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY T 49 " --> pdb=" O TRP T 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN T 59 " --> pdb=" O ARG T 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.613A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET T 81 " --> pdb=" O VAL T 20 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'Q' and resid 45 through 51 removed outlier: 6.207A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 63 through 65 1207 hydrogen bonds defined for protein. 3288 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: 7.22 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.34: 9444 1.34 - 1.51: 11660 1.51 - 1.69: 10279 1.69 - 1.86: 178 1.86 - 2.04: 1 Bond restraints: 31562 Sorted by residual: bond pdb=" CD2 PHE A 377 " pdb=" CE2 PHE A 377 " ideal model delta sigma weight residual 1.382 2.035 -0.653 3.00e-02 1.11e+03 4.74e+02 bond pdb=" C LEU A 368 " pdb=" N TYR A 369 " ideal model delta sigma weight residual 1.333 1.586 -0.253 1.41e-02 5.03e+03 3.21e+02 bond pdb=" C1 NAG A1313 " pdb=" O5 NAG A1313 " ideal model delta sigma weight residual 1.406 1.748 -0.342 2.00e-02 2.50e+03 2.92e+02 bond pdb=" N TYR A 369 " pdb=" CA TYR A 369 " ideal model delta sigma weight residual 1.460 1.653 -0.193 1.27e-02 6.20e+03 2.30e+02 bond pdb=" CA TYR A 369 " pdb=" C TYR A 369 " ideal model delta sigma weight residual 1.520 1.693 -0.173 1.37e-02 5.33e+03 1.59e+02 ... (remaining 31557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.75: 42811 7.75 - 15.49: 114 15.49 - 23.24: 8 23.24 - 30.98: 2 30.98 - 38.73: 3 Bond angle restraints: 42938 Sorted by residual: angle pdb=" C TYR A 369 " pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " ideal model delta sigma weight residual 109.16 74.98 34.18 1.29e+00 6.01e-01 7.02e+02 angle pdb=" C LEU A 368 " pdb=" N TYR A 369 " pdb=" CA TYR A 369 " ideal model delta sigma weight residual 121.52 160.25 -38.73 1.74e+00 3.30e-01 4.95e+02 angle pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " pdb=" CG TYR A 369 " ideal model delta sigma weight residual 113.90 145.21 -31.31 1.80e+00 3.09e-01 3.03e+02 angle pdb=" CD2 PHE A 377 " pdb=" CE2 PHE A 377 " pdb=" CZ PHE A 377 " ideal model delta sigma weight residual 120.00 89.06 30.94 1.80e+00 3.09e-01 2.96e+02 angle pdb=" CG PHE A 377 " pdb=" CD2 PHE A 377 " pdb=" CE2 PHE A 377 " ideal model delta sigma weight residual 120.70 143.76 -23.06 1.70e+00 3.46e-01 1.84e+02 ... (remaining 42933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16594 17.85 - 35.70: 1360 35.70 - 53.55: 235 53.55 - 71.40: 34 71.40 - 89.25: 32 Dihedral angle restraints: 18255 sinusoidal: 7051 harmonic: 11204 Sorted by residual: dihedral pdb=" C TYR A 369 " pdb=" N TYR A 369 " pdb=" CA TYR A 369 " pdb=" CB TYR A 369 " ideal model delta harmonic sigma weight residual -122.60 -91.91 -30.69 0 2.50e+00 1.60e-01 1.51e+02 dihedral pdb=" C VAL A 367 " pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" CB VAL A 367 " ideal model delta harmonic sigma weight residual -122.00 -141.06 19.06 0 2.50e+00 1.60e-01 5.81e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -150.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 18252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 4948 0.348 - 0.696: 30 0.696 - 1.044: 6 1.044 - 1.392: 2 1.392 - 1.740: 1 Chirality restraints: 4987 Sorted by residual: chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -0.66 -1.74 2.00e-01 2.50e+01 7.57e+01 chirality pdb=" C4 NAG A1313 " pdb=" C3 NAG A1313 " pdb=" C5 NAG A1313 " pdb=" O4 NAG A1313 " both_signs ideal model delta sigma weight residual False -2.53 -1.24 -1.29 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.48e+01 ... (remaining 4984 not shown) Planarity restraints: 5531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 377 " -0.180 2.00e-02 2.50e+03 1.69e-01 5.00e+02 pdb=" CG PHE A 377 " 0.210 2.00e-02 2.50e+03 pdb=" CD1 PHE A 377 " -0.154 2.00e-02 2.50e+03 pdb=" CD2 PHE A 377 " 0.254 2.00e-02 2.50e+03 pdb=" CE1 PHE A 377 " 0.072 2.00e-02 2.50e+03 pdb=" CE2 PHE A 377 " -0.170 2.00e-02 2.50e+03 pdb=" CZ PHE A 377 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 108 " -0.041 2.00e-02 2.50e+03 6.85e-02 9.37e+01 pdb=" CG TYR S 108 " 0.164 2.00e-02 2.50e+03 pdb=" CD1 TYR S 108 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR S 108 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR S 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 108 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR S 108 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR S 108 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 367 " 0.038 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" C VAL A 367 " -0.128 2.00e-02 2.50e+03 pdb=" O VAL A 367 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU A 368 " 0.042 2.00e-02 2.50e+03 ... (remaining 5528 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 340 2.61 - 3.19: 25350 3.19 - 3.76: 48401 3.76 - 4.33: 66277 4.33 - 4.90: 110519 Nonbonded interactions: 250887 Sorted by model distance: nonbonded pdb=" CE2 PHE A 377 " pdb=" O7 NAG A1313 " model vdw 2.042 2.672 nonbonded pdb=" OG1 THR R 120 " pdb=" O SER R 122 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR S 120 " pdb=" O SER S 122 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR T 120 " pdb=" O SER T 122 " model vdw 2.208 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.242 3.040 ... (remaining 250882 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 68 or resid 76 through 531 or (resid 532 throug \ h 533 and (name N or name CA or name C or name O or name CB )) or resid 534 thro \ ugh 577 or resid 584 through 1314)) selection = (chain 'B' and (resid 14 through 68 or resid 76 through 532 or (resid 533 and (n \ ame N or name CA or name C or name O or name CB )) or resid 534 through 577 or r \ esid 584 through 1314)) selection = (chain 'C' and resid 14 through 1314) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.120 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.310 Find NCS groups from input model: 0.840 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: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 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 : 0.010 0.653 31659 Z= 0.481 Angle : 1.341 38.729 43181 Z= 0.716 Chirality : 0.092 1.740 4987 Planarity : 0.009 0.169 5485 Dihedral : 13.398 89.247 10951 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.25 % 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: 3812 helix: 2.31 (0.20), residues: 675 sheet: 0.09 (0.17), residues: 906 loop : -1.28 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG C 357 TYR 0.164 0.004 TYR S 108 PHE 0.254 0.005 PHE A 377 TRP 0.042 0.004 TRP C 886 HIS 0.027 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.01012 / 0.47 (31562) covalent geometry : angle 1.30298 / 0.71 (42938) SS BOND : bond 0.00851 / 0.61 ( 42) SS BOND : angle 2.10755 / 1.42 ( 84) hydrogen bonds : bond 0.17184 / 11.19 ( 1143) hydrogen bonds : angle 7.71308 / 5.42 ( 3288) Misc. bond : bond 0.13173 / 6.30 ( 2) link_BETA1-4 : bond 0.00834 / 0.47 ( 7) link_BETA1-4 : angle 3.02379 / 1.97 ( 21) link_NAG-ASN : bond 0.01330 / 0.94 ( 46) link_NAG-ASN : angle 5.49854 / 4.08 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 177 MET cc_start: -0.0382 (mtt) cc_final: -0.1303 (mpp) REVERT: Q 87 TYR cc_start: 0.5786 (m-80) cc_final: 0.5188 (m-10) REVERT: Q 97 ARG cc_start: 0.4468 (mtp180) cc_final: 0.4178 (mmt180) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.6643 time to fit residues: 207.7192 Evaluate side-chains 130 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.0670 chunk 298 optimal weight: 2.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 196 ASN A 755 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 949 GLN B 955 ASN B1005 GLN B1011 GLN B1071 GLN C 146 HIS C 493 GLN C 544 ASN C 613 GLN C 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN S 6 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.093941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.077932 restraints weight = 219063.280| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 5.29 r_work: 0.3584 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 31659 Z= 0.193 Angle : 0.798 23.533 43181 Z= 0.387 Chirality : 0.054 0.965 4987 Planarity : 0.005 0.080 5485 Dihedral : 4.996 49.005 4170 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 1.17 % Allowed : 8.31 % Favored : 90.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.32 (0.14), residues: 3812 helix: 2.25 (0.20), residues: 674 sheet: 0.17 (0.17), residues: 852 loop : -1.18 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 567 TYR 0.046 0.002 TYR S 108 PHE 0.077 0.002 PHE A 377 TRP 0.011 0.002 TRP R 113 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (31562) covalent geometry : angle 0.77040 / 0.38 (42938) SS BOND : bond 0.00362 / 0.24 ( 42) SS BOND : angle 0.92038 / 0.61 ( 84) hydrogen bonds : bond 0.04350 / 2.84 ( 1143) hydrogen bonds : angle 6.01350 / 4.22 ( 3288) Misc. bond : bond 0.03487 / 1.67 ( 2) link_BETA1-4 : bond 0.00658 / 0.36 ( 7) link_BETA1-4 : angle 1.55239 / 1.00 ( 21) link_NAG-ASN : bond 0.00615 / 0.42 ( 46) link_NAG-ASN : angle 3.70639 / 2.87 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 988 GLU cc_start: 0.9330 (mp0) cc_final: 0.9088 (mp0) REVERT: B 505 TYR cc_start: 0.8960 (m-10) cc_final: 0.8560 (t80) REVERT: C 177 MET cc_start: -0.1330 (mtt) cc_final: -0.1692 (mpt) REVERT: C 456 PHE cc_start: 0.9468 (m-80) cc_final: 0.9210 (m-80) REVERT: C 505 TYR cc_start: 0.9437 (m-80) cc_final: 0.9111 (t80) REVERT: S 81 MET cc_start: 0.7518 (ptm) cc_final: 0.6477 (ppp) outliers start: 39 outliers final: 8 residues processed: 159 average time/residue: 0.6219 time to fit residues: 117.3243 Evaluate side-chains 122 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain Q residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 295 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 380 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A1005 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B 764 ASN P 39 GLN P 43 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.075765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.047983 restraints weight = 231474.725| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 8.68 r_work: 0.3321 rms_B_bonded: 7.14 restraints_weight: 2.0000 r_work: 0.3412 rms_B_bonded: 5.22 restraints_weight: 4.0000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.265 31659 Z= 0.303 Angle : 0.861 27.427 43181 Z= 0.422 Chirality : 0.057 1.269 4987 Planarity : 0.005 0.130 5485 Dihedral : 5.060 42.269 4170 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.36 % Rotamer: Outliers : 2.14 % Allowed : 9.99 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3812 helix: 2.03 (0.20), residues: 673 sheet: -0.30 (0.17), residues: 873 loop : -1.25 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 44 TYR 0.032 0.002 TYR S 108 PHE 0.032 0.002 PHE A 374 TRP 0.025 0.003 TRP T 47 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.30 (31562) covalent geometry : angle 0.83296 / 0.42 (42938) SS BOND : bond 0.00571 / 0.40 ( 42) SS BOND : angle 1.18774 / 0.81 ( 84) hydrogen bonds : bond 0.04886 / 3.22 ( 1143) hydrogen bonds : angle 6.10731 / 4.29 ( 3288) Misc. bond : bond 0.03106 / 1.49 ( 2) link_BETA1-4 : bond 0.00398 / 0.20 ( 7) link_BETA1-4 : angle 1.45677 / 0.88 ( 21) link_NAG-ASN : bond 0.00802 / 0.54 ( 46) link_NAG-ASN : angle 3.87558 / 2.99 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 126 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1005 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8492 (tp-100) REVERT: C 177 MET cc_start: -0.0123 (mtt) cc_final: -0.1078 (mpt) REVERT: C 564 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8272 (tp40) REVERT: C 755 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7907 (pp30) REVERT: R 48 MET cc_start: 0.8386 (mpp) cc_final: 0.8128 (mpp) REVERT: R 81 MET cc_start: 0.5585 (mtm) cc_final: 0.5211 (mmm) REVERT: S 81 MET cc_start: 0.8469 (ptm) cc_final: 0.7374 (ppp) REVERT: P 59 ILE cc_start: 0.4287 (OUTLIER) cc_final: 0.4006 (pt) outliers start: 71 outliers final: 24 residues processed: 178 average time/residue: 0.5558 time to fit residues: 118.5048 Evaluate side-chains 123 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain Q residue 33 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 98 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 284 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 564 GLN B 644 GLN C 146 HIS C 493 GLN C 606 ASN C1071 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.083439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.066404 restraints weight = 212378.597| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 5.36 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 31659 Z= 0.144 Angle : 0.691 20.468 43181 Z= 0.334 Chirality : 0.050 0.507 4987 Planarity : 0.004 0.060 5485 Dihedral : 4.773 40.424 4170 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.44 % Rotamer: Outliers : 1.72 % Allowed : 11.68 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.45 (0.13), residues: 3812 helix: 2.33 (0.20), residues: 672 sheet: -0.16 (0.17), residues: 875 loop : -1.22 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.024 0.001 TYR S 108 PHE 0.026 0.001 PHE A 374 TRP 0.014 0.001 TRP S 47 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (31562) covalent geometry : angle 0.66427 / 0.33 (42938) SS BOND : bond 0.00302 / 0.21 ( 42) SS BOND : angle 0.79266 / 0.56 ( 84) hydrogen bonds : bond 0.03917 / 2.62 ( 1143) hydrogen bonds : angle 5.69408 / 4.02 ( 3288) Misc. bond : bond 0.01823 / 0.88 ( 2) link_BETA1-4 : bond 0.00588 / 0.34 ( 7) link_BETA1-4 : angle 1.34255 / 0.81 ( 21) link_NAG-ASN : bond 0.00601 / 0.40 ( 46) link_NAG-ASN : angle 3.38673 / 2.60 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7564 (p) REVERT: B 166 CYS cc_start: 0.5830 (OUTLIER) cc_final: 0.5454 (m) REVERT: B 388 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7393 (p0) REVERT: B 505 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8694 (t80) REVERT: B 773 GLU cc_start: 0.8236 (tp30) cc_final: 0.7808 (tp30) REVERT: B 1005 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8034 (tp-100) REVERT: S 81 MET cc_start: 0.6691 (ptm) cc_final: 0.6416 (ppp) REVERT: P 72 PHE cc_start: 0.8496 (p90) cc_final: 0.8180 (p90) REVERT: P 78 ARG cc_start: 0.8355 (tpm170) cc_final: 0.8135 (tpm170) REVERT: Q 2 ILE cc_start: 0.0348 (OUTLIER) cc_final: 0.0035 (tt) REVERT: Q 11 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5081 (pt) outliers start: 57 outliers final: 12 residues processed: 150 average time/residue: 0.7338 time to fit residues: 130.2100 Evaluate side-chains 109 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 50 ARG Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 11 LEU Chi-restraints excluded: chain Q residue 33 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 218 optimal weight: 9.9990 chunk 328 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 343 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 378 optimal weight: 40.0000 chunk 49 optimal weight: 0.8980 chunk 371 optimal weight: 30.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 913 GLN A1088 HIS ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 52 GLN C 121 ASN C1088 HIS ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.070721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.042592 restraints weight = 235367.114| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 8.38 r_work: 0.3147 rms_B_bonded: 7.41 restraints_weight: 2.0000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.182 31659 Z= 0.553 Angle : 1.094 21.141 43181 Z= 0.549 Chirality : 0.059 0.608 4987 Planarity : 0.007 0.076 5485 Dihedral : 6.230 48.789 4170 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.35 % Favored : 92.60 % Rotamer: Outliers : 3.01 % Allowed : 12.70 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 3812 helix: 1.01 (0.19), residues: 678 sheet: -0.92 (0.16), residues: 909 loop : -1.60 (0.12), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 102 TYR 0.061 0.004 TYR A 369 PHE 0.049 0.004 PHE A 377 TRP 0.032 0.004 TRP R 36 HIS 0.009 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.01186 / 0.55 (31562) covalent geometry : angle 1.06860 / 0.54 (42938) SS BOND : bond 0.01149 / 0.77 ( 42) SS BOND : angle 1.90340 / 1.25 ( 84) hydrogen bonds : bond 0.06110 / 4.08 ( 1143) hydrogen bonds : angle 7.08496 / 4.99 ( 3288) Misc. bond : bond 0.00817 / 0.40 ( 2) link_BETA1-4 : bond 0.00591 / 0.33 ( 7) link_BETA1-4 : angle 1.60780 / 0.94 ( 21) link_NAG-ASN : bond 0.01105 / 0.71 ( 46) link_NAG-ASN : angle 4.06256 / 3.15 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 113 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.9436 (m-30) cc_final: 0.8833 (t0) REVERT: A 900 MET cc_start: 0.8937 (mmm) cc_final: 0.8633 (mtt) REVERT: B 63 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7601 (p) REVERT: B 226 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8301 (mp) REVERT: B 697 MET cc_start: 0.8962 (ptp) cc_final: 0.8639 (ptm) REVERT: B 754 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9202 (pt) REVERT: C 177 MET cc_start: 0.6286 (mpp) cc_final: 0.5650 (mpp) REVERT: C 200 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8819 (t80) REVERT: C 490 PHE cc_start: 0.9343 (t80) cc_final: 0.9068 (t80) REVERT: R 81 MET cc_start: 0.3660 (OUTLIER) cc_final: 0.3439 (mmt) REVERT: S 48 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6793 (pmm) REVERT: S 81 MET cc_start: 0.8089 (ptm) cc_final: 0.6876 (ppp) outliers start: 100 outliers final: 35 residues processed: 193 average time/residue: 0.5564 time to fit residues: 132.5466 Evaluate side-chains 135 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain T residue 50 ARG Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain Q residue 80 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 302 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 374 optimal weight: 0.0070 chunk 99 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 188 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 87 ASN B 271 GLN B 331 ASN B 388 ASN B 564 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.072754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.046090 restraints weight = 228415.170| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 8.25 r_work: 0.3209 rms_B_bonded: 7.20 restraints_weight: 2.0000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.6659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 31659 Z= 0.157 Angle : 0.759 21.701 43181 Z= 0.367 Chirality : 0.051 0.621 4987 Planarity : 0.005 0.069 5485 Dihedral : 5.357 55.515 4170 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 1.72 % Allowed : 14.78 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.94 (0.13), residues: 3812 helix: 2.09 (0.20), residues: 660 sheet: -0.72 (0.17), residues: 878 loop : -1.47 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 62 TYR 0.065 0.002 TYR A 369 PHE 0.042 0.002 PHE A 374 TRP 0.013 0.002 TRP Q 36 HIS 0.007 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (31562) covalent geometry : angle 0.73171 / 0.36 (42938) SS BOND : bond 0.00352 / 0.25 ( 42) SS BOND : angle 1.06993 / 0.78 ( 84) hydrogen bonds : bond 0.04238 / 2.84 ( 1143) hydrogen bonds : angle 6.15496 / 4.35 ( 3288) Misc. bond : bond 0.01616 / 0.79 ( 2) link_BETA1-4 : bond 0.00408 / 0.25 ( 7) link_BETA1-4 : angle 1.28937 / 0.76 ( 21) link_NAG-ASN : bond 0.00738 / 0.49 ( 46) link_NAG-ASN : angle 3.54918 / 2.73 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 100 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2911 (mpt) cc_final: 0.2438 (mpt) REVERT: B 191 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 350 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8883 (p) REVERT: B 388 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7707 (p0) REVERT: B 754 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9099 (pp) REVERT: C 177 MET cc_start: 0.5792 (mpp) cc_final: 0.5508 (mpt) REVERT: C 265 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.5746 (p90) REVERT: R 81 MET cc_start: 0.3934 (mmm) cc_final: 0.3717 (mmt) REVERT: S 48 MET cc_start: 0.7212 (pmt) cc_final: 0.6709 (pmm) REVERT: S 81 MET cc_start: 0.8172 (ptm) cc_final: 0.7070 (ppp) outliers start: 57 outliers final: 18 residues processed: 147 average time/residue: 0.6538 time to fit residues: 116.0770 Evaluate side-chains 111 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 295 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 319 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 388 ASN B 544 ASN B 564 GLN B1011 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.071581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.044306 restraints weight = 230526.359| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 8.31 r_work: 0.3185 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31659 Z= 0.238 Angle : 0.774 20.462 43181 Z= 0.372 Chirality : 0.053 1.169 4987 Planarity : 0.005 0.062 5485 Dihedral : 5.231 51.704 4170 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 1.54 % Allowed : 15.35 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.87 (0.13), residues: 3812 helix: 2.24 (0.20), residues: 661 sheet: -0.71 (0.17), residues: 881 loop : -1.45 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 457 TYR 0.045 0.002 TYR A 369 PHE 0.043 0.002 PHE A 374 TRP 0.013 0.002 TRP C 104 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.24 (31562) covalent geometry : angle 0.74250 / 0.37 (42938) SS BOND : bond 0.00521 / 0.34 ( 42) SS BOND : angle 1.11057 / 0.74 ( 84) hydrogen bonds : bond 0.04307 / 2.92 ( 1143) hydrogen bonds : angle 6.09684 / 4.31 ( 3288) Misc. bond : bond 0.01380 / 0.67 ( 2) link_BETA1-4 : bond 0.00455 / 0.26 ( 7) link_BETA1-4 : angle 1.23397 / 0.73 ( 21) link_NAG-ASN : bond 0.00566 / 0.39 ( 46) link_NAG-ASN : angle 3.86997 / 2.98 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1279 (mpt) cc_final: 0.0809 (mpt) REVERT: A 198 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.7887 (t70) REVERT: B 350 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9033 (p) REVERT: B 388 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8267 (p0) REVERT: B 754 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9124 (pp) REVERT: C 177 MET cc_start: 0.4483 (mpp) cc_final: 0.4215 (mpt) REVERT: C 265 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6229 (p90) REVERT: C 697 MET cc_start: 0.9077 (ttm) cc_final: 0.8776 (mtm) REVERT: R 81 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4867 (mmt) REVERT: S 48 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6793 (pmt) REVERT: S 81 MET cc_start: 0.8287 (ptm) cc_final: 0.7442 (ppp) outliers start: 51 outliers final: 22 residues processed: 135 average time/residue: 0.5582 time to fit residues: 92.9354 Evaluate side-chains 119 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain T residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 48 optimal weight: 0.8980 chunk 333 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 343 optimal weight: 0.2980 chunk 264 optimal weight: 0.0980 chunk 19 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 388 ASN C 239 GLN C 710 ASN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.072455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.045354 restraints weight = 227177.609| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 8.35 r_work: 0.3238 rms_B_bonded: 6.60 restraints_weight: 2.0000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.6988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31659 Z= 0.136 Angle : 0.713 19.056 43181 Z= 0.340 Chirality : 0.050 0.696 4987 Planarity : 0.004 0.050 5485 Dihedral : 4.964 47.365 4170 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 1.35 % Allowed : 15.47 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.73 (0.13), residues: 3812 helix: 2.41 (0.20), residues: 662 sheet: -0.63 (0.17), residues: 880 loop : -1.37 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 457 TYR 0.049 0.001 TYR C 505 PHE 0.046 0.001 PHE A 374 TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (31562) covalent geometry : angle 0.68476 / 0.33 (42938) SS BOND : bond 0.00279 / 0.19 ( 42) SS BOND : angle 0.83208 / 0.56 ( 84) hydrogen bonds : bond 0.03815 / 2.57 ( 1143) hydrogen bonds : angle 5.79280 / 4.10 ( 3288) Misc. bond : bond 0.01247 / 0.61 ( 2) link_BETA1-4 : bond 0.00362 / 0.20 ( 7) link_BETA1-4 : angle 1.15653 / 0.68 ( 21) link_NAG-ASN : bond 0.00616 / 0.41 ( 46) link_NAG-ASN : angle 3.52837 / 2.72 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1792 (mpt) cc_final: 0.1208 (mpt) REVERT: A 198 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.8098 (t70) REVERT: B 350 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8885 (p) REVERT: B 387 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7605 (tp) REVERT: B 740 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8798 (ppp) REVERT: B 754 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9058 (pp) REVERT: B 773 GLU cc_start: 0.8657 (tp30) cc_final: 0.8141 (tp30) REVERT: C 177 MET cc_start: 0.5519 (mpp) cc_final: 0.5099 (mpt) REVERT: C 265 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.5997 (p90) REVERT: C 697 MET cc_start: 0.9003 (ttm) cc_final: 0.8713 (mtm) REVERT: R 81 MET cc_start: 0.5047 (OUTLIER) cc_final: 0.4636 (mmt) REVERT: S 48 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6408 (pmm) REVERT: S 81 MET cc_start: 0.8317 (ptm) cc_final: 0.7516 (ppp) REVERT: T 48 MET cc_start: 0.6649 (pmm) cc_final: 0.6345 (pmm) outliers start: 45 outliers final: 20 residues processed: 131 average time/residue: 0.5751 time to fit residues: 92.4336 Evaluate side-chains 119 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 99 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 370 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 351 optimal weight: 0.0370 chunk 214 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN C 196 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.070714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.043439 restraints weight = 229623.889| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 7.72 r_work: 0.3158 rms_B_bonded: 6.58 restraints_weight: 2.0000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.7546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31659 Z= 0.253 Angle : 0.771 18.312 43181 Z= 0.374 Chirality : 0.051 0.616 4987 Planarity : 0.005 0.055 5485 Dihedral : 5.099 41.962 4170 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 1.26 % Allowed : 15.83 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.13), residues: 3812 helix: 2.44 (0.20), residues: 655 sheet: -0.74 (0.17), residues: 905 loop : -1.37 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 78 TYR 0.035 0.002 TYR A 369 PHE 0.052 0.002 PHE A 374 TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (31562) covalent geometry : angle 0.74463 / 0.37 (42938) SS BOND : bond 0.00612 / 0.40 ( 42) SS BOND : angle 1.22373 / 0.80 ( 84) hydrogen bonds : bond 0.04349 / 2.96 ( 1143) hydrogen bonds : angle 6.01022 / 4.24 ( 3288) Misc. bond : bond 0.01150 / 0.56 ( 2) link_BETA1-4 : bond 0.00444 / 0.25 ( 7) link_BETA1-4 : angle 1.24117 / 0.74 ( 21) link_NAG-ASN : bond 0.00623 / 0.42 ( 46) link_NAG-ASN : angle 3.53737 / 2.77 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.9185 (m-30) cc_final: 0.8984 (p0) REVERT: A 177 MET cc_start: 0.3360 (mpt) cc_final: 0.2708 (mpt) REVERT: A 1074 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8394 (m110) REVERT: B 350 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8836 (p) REVERT: B 754 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9146 (pp) REVERT: C 63 THR cc_start: 0.6806 (m) cc_final: 0.6551 (t) REVERT: C 177 MET cc_start: 0.6481 (mpp) cc_final: 0.6016 (mpt) REVERT: C 265 TYR cc_start: 0.6183 (OUTLIER) cc_final: 0.5892 (p90) REVERT: C 490 PHE cc_start: 0.9327 (t80) cc_final: 0.9045 (t80) REVERT: C 697 MET cc_start: 0.9111 (ttm) cc_final: 0.8781 (mtm) REVERT: R 48 MET cc_start: 0.7465 (mpp) cc_final: 0.7021 (pmm) REVERT: S 48 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6206 (pmm) REVERT: S 54 MET cc_start: 0.9669 (ppp) cc_final: 0.9303 (ppp) REVERT: S 81 MET cc_start: 0.8200 (ptm) cc_final: 0.7350 (ppp) REVERT: T 48 MET cc_start: 0.7300 (pmm) cc_final: 0.7023 (pmm) outliers start: 42 outliers final: 22 residues processed: 132 average time/residue: 0.5715 time to fit residues: 92.6294 Evaluate side-chains 117 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 258 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 368 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 180 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.071339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.044266 restraints weight = 227826.141| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 8.35 r_work: 0.3186 rms_B_bonded: 7.18 restraints_weight: 2.0000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31659 Z= 0.156 Angle : 0.714 18.071 43181 Z= 0.343 Chirality : 0.050 0.565 4987 Planarity : 0.004 0.051 5485 Dihedral : 4.911 40.086 4170 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 1.02 % Allowed : 16.20 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.13), residues: 3812 helix: 2.54 (0.20), residues: 660 sheet: -0.63 (0.17), residues: 869 loop : -1.36 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 87 TYR 0.034 0.001 TYR A 369 PHE 0.052 0.001 PHE A 374 TRP 0.032 0.002 TRP C 104 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (31562) covalent geometry : angle 0.68732 / 0.34 (42938) SS BOND : bond 0.00368 / 0.25 ( 42) SS BOND : angle 0.95786 / 0.65 ( 84) hydrogen bonds : bond 0.03852 / 2.62 ( 1143) hydrogen bonds : angle 5.81922 / 4.11 ( 3288) Misc. bond : bond 0.01057 / 0.52 ( 2) link_BETA1-4 : bond 0.00361 / 0.20 ( 7) link_BETA1-4 : angle 1.15168 / 0.68 ( 21) link_NAG-ASN : bond 0.00560 / 0.38 ( 46) link_NAG-ASN : angle 3.39999 / 2.66 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3193 (mpt) cc_final: 0.2527 (mpt) REVERT: A 198 ASP cc_start: 0.9629 (OUTLIER) cc_final: 0.8522 (t0) REVERT: B 754 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9177 (pp) REVERT: B 773 GLU cc_start: 0.8656 (tp30) cc_final: 0.8202 (tp30) REVERT: C 63 THR cc_start: 0.6833 (m) cc_final: 0.6580 (t) REVERT: C 177 MET cc_start: 0.6542 (mpp) cc_final: 0.6051 (mpt) REVERT: C 265 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.5879 (p90) REVERT: C 490 PHE cc_start: 0.9274 (t80) cc_final: 0.9063 (t80) REVERT: C 697 MET cc_start: 0.9086 (ttm) cc_final: 0.8827 (mtm) REVERT: S 48 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6196 (pmm) REVERT: S 81 MET cc_start: 0.8308 (ptm) cc_final: 0.7487 (ppp) REVERT: T 48 MET cc_start: 0.7224 (pmm) cc_final: 0.6955 (pmm) outliers start: 34 outliers final: 21 residues processed: 127 average time/residue: 0.5912 time to fit residues: 91.8193 Evaluate side-chains 117 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 144 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 180 optimal weight: 0.0030 chunk 174 optimal weight: 0.5980 chunk 299 optimal weight: 3.9990 chunk 357 optimal weight: 9.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.071103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.044015 restraints weight = 229343.070| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 8.13 r_work: 0.3186 rms_B_bonded: 6.60 restraints_weight: 2.0000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31659 Z= 0.172 Angle : 0.716 18.393 43181 Z= 0.344 Chirality : 0.050 0.536 4987 Planarity : 0.004 0.058 5485 Dihedral : 4.875 38.514 4170 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 1.11 % Allowed : 16.13 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.14), residues: 3812 helix: 2.49 (0.20), residues: 666 sheet: -0.62 (0.17), residues: 899 loop : -1.36 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 457 TYR 0.050 0.002 TYR B 505 PHE 0.051 0.001 PHE A 374 TRP 0.028 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (31562) covalent geometry : angle 0.69021 / 0.34 (42938) SS BOND : bond 0.00408 / 0.27 ( 42) SS BOND : angle 1.01537 / 0.68 ( 84) hydrogen bonds : bond 0.03876 / 2.64 ( 1143) hydrogen bonds : angle 5.77644 / 4.08 ( 3288) Misc. bond : bond 0.01017 / 0.50 ( 2) link_BETA1-4 : bond 0.00451 / 0.25 ( 7) link_BETA1-4 : angle 1.15084 / 0.69 ( 21) link_NAG-ASN : bond 0.00550 / 0.37 ( 46) link_NAG-ASN : angle 3.38015 / 2.64 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18853.32 seconds wall clock time: 319 minutes 49.24 seconds (19189.24 seconds total)