Starting phenix.real_space_refine on Fri Mar 6 12:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a95_15270/03_2026/8a95_15270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a95_15270/03_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_15270/03_2026/8a95_15270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a95_15270/03_2026/8a95_15270.map" model { file = "/net/cci-nas-00/data/ceres_data/8a95_15270/03_2026/8a95_15270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a95_15270/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 42 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 dihedrals: 45 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 dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 7.45, per 1000 atoms: 0.24 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: 2.66 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: 1.18 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: 9.65 Time building geometry restraints manager: 2.99 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 - 24.59: 18390 24.59 - 49.18: 932 49.18 - 73.77: 111 73.77 - 98.36: 48 98.36 - 122.94: 13 Dihedral angle restraints: 19494 sinusoidal: 8290 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 19491 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: 12.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 31.600 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 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 : 14.676 122.945 12190 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 covalent geometry : bond 0.01012 (31562) covalent geometry : angle 1.30298 (42938) SS BOND : bond 0.00851 ( 42) SS BOND : angle 2.10755 ( 84) hydrogen bonds : bond 0.17184 ( 1143) hydrogen bonds : angle 7.71308 ( 3288) Misc. bond : bond 0.13173 ( 2) link_BETA1-4 : bond 0.00834 ( 7) link_BETA1-4 : angle 3.02379 ( 21) link_NAG-ASN : bond 0.01330 ( 46) link_NAG-ASN : angle 5.49854 ( 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 : 0.990 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: 0.7467 time to fit residues: 231.9902 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 : 1.135 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4397 r_free = 0.4397 target = 0.094451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.078545 restraints weight = 219693.222| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 5.21 r_work: 0.3583 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 31659 Z= 0.193 Angle : 0.804 24.020 43181 Z= 0.389 Chirality : 0.054 0.847 4987 Planarity : 0.005 0.079 5485 Dihedral : 9.774 108.335 5409 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 1.14 % Allowed : 8.46 % Favored : 90.40 % 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: -0.34 (0.13), residues: 3812 helix: 2.19 (0.20), residues: 680 sheet: 0.16 (0.17), residues: 849 loop : -1.19 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 62 TYR 0.048 0.002 TYR S 108 PHE 0.082 0.002 PHE A 377 TRP 0.014 0.002 TRP Q 36 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00407 (31562) covalent geometry : angle 0.77478 (42938) SS BOND : bond 0.00378 ( 42) SS BOND : angle 0.93247 ( 84) hydrogen bonds : bond 0.04298 ( 1143) hydrogen bonds : angle 5.99701 ( 3288) Misc. bond : bond 0.03915 ( 2) link_BETA1-4 : bond 0.00690 ( 7) link_BETA1-4 : angle 2.28062 ( 21) link_NAG-ASN : bond 0.00634 ( 46) link_NAG-ASN : angle 3.76507 ( 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: 38 poor density : 138 time to evaluate : 1.176 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: 0.9400 (mp0) cc_final: 0.9150 (mp0) REVERT: B 505 TYR cc_start: 0.8987 (m-10) cc_final: 0.8580 (t80) REVERT: C 177 MET cc_start: -0.1227 (mtt) cc_final: -0.1656 (mpt) REVERT: C 456 PHE cc_start: 0.9519 (m-80) cc_final: 0.9245 (m-80) REVERT: C 505 TYR cc_start: 0.9468 (m-80) cc_final: 0.9144 (t80) REVERT: S 81 MET cc_start: 0.7428 (ptm) cc_final: 0.6464 (ppp) outliers start: 38 outliers final: 8 residues processed: 160 average time/residue: 0.7381 time to fit residues: 138.2192 Evaluate side-chains 120 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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: 0.9980 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 380 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** P 101 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.075389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.047818 restraints weight = 231450.888| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 8.22 r_work: 0.3296 rms_B_bonded: 6.93 restraints_weight: 2.0000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.202 31659 Z= 0.318 Angle : 0.908 34.080 43181 Z= 0.442 Chirality : 0.055 0.774 4987 Planarity : 0.006 0.145 5485 Dihedral : 8.507 94.799 5409 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 2.23 % Allowed : 10.33 % Favored : 87.45 % 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: -0.68 (0.13), residues: 3812 helix: 1.95 (0.20), residues: 673 sheet: -0.36 (0.17), residues: 869 loop : -1.29 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 408 TYR 0.035 0.003 TYR Q 33 PHE 0.032 0.003 PHE C 562 TRP 0.026 0.003 TRP T 47 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00683 (31562) covalent geometry : angle 0.87755 (42938) SS BOND : bond 0.00628 ( 42) SS BOND : angle 1.28627 ( 84) hydrogen bonds : bond 0.05072 ( 1143) hydrogen bonds : angle 6.19993 ( 3288) Misc. bond : bond 0.02991 ( 2) link_BETA1-4 : bond 0.00502 ( 7) link_BETA1-4 : angle 2.18207 ( 21) link_NAG-ASN : bond 0.00853 ( 46) link_NAG-ASN : angle 4.08502 ( 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 196 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 122 time to evaluate : 1.149 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: A 237 ARG cc_start: 0.8906 (mtp-110) cc_final: 0.8693 (mtm110) REVERT: B 90 VAL cc_start: 0.5389 (OUTLIER) cc_final: 0.4507 (p) REVERT: B 1005 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8630 (tp-100) REVERT: C 177 MET cc_start: 0.0121 (mtt) cc_final: -0.0839 (mpp) REVERT: C 564 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8252 (tp40) REVERT: C 755 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8027 (pp30) REVERT: R 48 MET cc_start: 0.8514 (mpp) cc_final: 0.8267 (mpp) REVERT: S 81 MET cc_start: 0.8408 (ptm) cc_final: 0.7209 (ppp) REVERT: P 59 ILE cc_start: 0.3898 (OUTLIER) cc_final: 0.3580 (pt) REVERT: P 62 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8525 (ptt90) outliers start: 74 outliers final: 23 residues processed: 178 average time/residue: 0.6444 time to fit residues: 136.8413 Evaluate side-chains 125 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 480 CYS 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 50 TYR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain P residue 59 ILE Chi-restraints excluded: chain P residue 62 ARG 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: 5.9990 chunk 284 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 265 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4585 r_free = 0.4585 target = 0.076166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.048961 restraints weight = 227659.922| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 8.00 r_work: 0.3326 rms_B_bonded: 6.71 restraints_weight: 2.0000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 31659 Z= 0.153 Angle : 0.703 20.131 43181 Z= 0.338 Chirality : 0.050 0.526 4987 Planarity : 0.004 0.077 5485 Dihedral : 7.531 83.906 5409 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.44 % Rotamer: Outliers : 1.60 % Allowed : 11.95 % Favored : 86.45 % 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: -0.48 (0.13), residues: 3812 helix: 2.35 (0.20), residues: 669 sheet: -0.21 (0.17), residues: 875 loop : -1.24 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 403 TYR 0.030 0.001 TYR A 365 PHE 0.025 0.001 PHE A 374 TRP 0.016 0.002 TRP S 47 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00325 (31562) covalent geometry : angle 0.67298 (42938) SS BOND : bond 0.00317 ( 42) SS BOND : angle 0.83729 ( 84) hydrogen bonds : bond 0.03987 ( 1143) hydrogen bonds : angle 5.74077 ( 3288) Misc. bond : bond 0.01770 ( 2) link_BETA1-4 : bond 0.00478 ( 7) link_BETA1-4 : angle 2.11048 ( 21) link_NAG-ASN : bond 0.00591 ( 46) link_NAG-ASN : angle 3.54587 ( 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 165 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.212 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: B 63 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7372 (p) REVERT: B 388 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 505 TYR cc_start: 0.9545 (OUTLIER) cc_final: 0.9145 (t80) REVERT: B 740 MET cc_start: 0.8965 (ppp) cc_final: 0.8748 (ppp) REVERT: B 1005 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8536 (tp-100) REVERT: C 177 MET cc_start: -0.0221 (mtt) cc_final: -0.1092 (mpp) REVERT: C 564 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8183 (tp40) REVERT: R 48 MET cc_start: 0.8009 (mpp) cc_final: 0.7773 (mpp) REVERT: S 81 MET cc_start: 0.8077 (ptm) cc_final: 0.7056 (ppp) REVERT: P 62 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8613 (ptt90) REVERT: T 81 MET cc_start: 0.4502 (mmm) cc_final: 0.4024 (mmm) REVERT: T 83 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6402 (mm) REVERT: T 91 THR cc_start: 0.8579 (p) cc_final: 0.8351 (m) outliers start: 53 outliers final: 12 residues processed: 150 average time/residue: 0.6847 time to fit residues: 121.5121 Evaluate side-chains 116 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 213 VAL 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 552 LEU 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 P residue 62 ARG Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 83 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: 10.0000 chunk 328 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 343 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 371 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 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 B1011 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN ** 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 = 0.4464 r_free = 0.4464 target = 0.071860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.043876 restraints weight = 232923.130| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 8.67 r_work: 0.3192 rms_B_bonded: 6.82 restraints_weight: 2.0000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 31659 Z= 0.394 Angle : 0.925 25.324 43181 Z= 0.458 Chirality : 0.054 0.557 4987 Planarity : 0.006 0.064 5485 Dihedral : 7.696 61.824 5409 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.00 % Rotamer: Outliers : 2.59 % Allowed : 12.94 % Favored : 84.47 % 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: -1.01 (0.13), residues: 3812 helix: 1.56 (0.20), residues: 687 sheet: -0.70 (0.17), residues: 887 loop : -1.42 (0.12), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 50 TYR 0.075 0.003 TYR A 369 PHE 0.033 0.003 PHE C 106 TRP 0.020 0.003 TRP S 47 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00841 (31562) covalent geometry : angle 0.89676 (42938) SS BOND : bond 0.00852 ( 42) SS BOND : angle 1.58858 ( 84) hydrogen bonds : bond 0.05357 ( 1143) hydrogen bonds : angle 6.58312 ( 3288) Misc. bond : bond 0.01223 ( 2) link_BETA1-4 : bond 0.00499 ( 7) link_BETA1-4 : angle 2.05827 ( 21) link_NAG-ASN : bond 0.00782 ( 46) link_NAG-ASN : angle 3.92227 ( 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 201 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 115 time to evaluate : 1.149 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: B 63 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7889 (p) REVERT: B 388 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8635 (p0) REVERT: B 754 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9153 (pt) REVERT: B 756 TYR cc_start: 0.8863 (t80) cc_final: 0.8659 (t80) REVERT: C 177 MET cc_start: 0.0542 (mtt) cc_final: -0.0103 (mtt) REVERT: C 564 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8401 (tp-100) REVERT: C 755 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7823 (pp30) REVERT: R 81 MET cc_start: 0.4559 (mmm) cc_final: 0.4301 (mmt) REVERT: O 59 ILE cc_start: 0.3525 (OUTLIER) cc_final: 0.3193 (pt) REVERT: S 81 MET cc_start: 0.8351 (ptm) cc_final: 0.7220 (ppp) REVERT: P 62 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8396 (ttt180) REVERT: T 81 MET cc_start: 0.4286 (mmm) cc_final: 0.3973 (mmm) outliers start: 86 outliers final: 26 residues processed: 185 average time/residue: 0.5825 time to fit residues: 130.1689 Evaluate side-chains 131 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 388 ASN 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 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 755 GLN 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 18 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain Q residue 33 TYR 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: 0.7980 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 374 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 87 ASN B 271 GLN B 564 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 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 = 0.4502 r_free = 0.4502 target = 0.073349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.045925 restraints weight = 228333.422| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 8.56 r_work: 0.3267 rms_B_bonded: 6.85 restraints_weight: 2.0000 r_work: 0.3369 rms_B_bonded: 5.87 restraints_weight: 4.0000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 31659 Z= 0.143 Angle : 0.738 19.706 43181 Z= 0.351 Chirality : 0.051 0.555 4987 Planarity : 0.004 0.076 5485 Dihedral : 7.040 58.072 5409 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 1.72 % Allowed : 14.54 % Favored : 83.74 % 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: -0.76 (0.13), residues: 3812 helix: 2.23 (0.20), residues: 663 sheet: -0.56 (0.17), residues: 860 loop : -1.37 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 87 TYR 0.067 0.002 TYR A 369 PHE 0.045 0.002 PHE A 374 TRP 0.015 0.002 TRP S 47 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (31562) covalent geometry : angle 0.70766 (42938) SS BOND : bond 0.00360 ( 42) SS BOND : angle 0.94052 ( 84) hydrogen bonds : bond 0.04096 ( 1143) hydrogen bonds : angle 5.95351 ( 3288) Misc. bond : bond 0.01321 ( 2) link_BETA1-4 : bond 0.00320 ( 7) link_BETA1-4 : angle 2.00728 ( 21) link_NAG-ASN : bond 0.00620 ( 46) link_NAG-ASN : angle 3.66310 ( 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 161 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 104 time to evaluate : 0.885 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: 0.2848 (mpt) cc_final: 0.2390 (mpt) REVERT: A 198 ASP cc_start: 0.9091 (m-30) cc_final: 0.7873 (t70) REVERT: A 1002 GLN cc_start: 0.9129 (tp40) cc_final: 0.8924 (tp-100) REVERT: B 350 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8835 (p) REVERT: B 754 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8915 (pp) REVERT: C 177 MET cc_start: 0.1347 (mtt) cc_final: 0.0184 (mtt) REVERT: C 265 TYR cc_start: 0.5745 (OUTLIER) cc_final: 0.5484 (p90) REVERT: C 564 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8227 (tp-100) REVERT: C 755 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7770 (pp30) REVERT: S 48 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7445 (pmm) REVERT: S 81 MET cc_start: 0.8421 (ptm) cc_final: 0.7596 (ppp) REVERT: T 81 MET cc_start: 0.4659 (mmm) cc_final: 0.4327 (mmm) REVERT: T 83 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6107 (mm) outliers start: 57 outliers final: 19 residues processed: 149 average time/residue: 0.6286 time to fit residues: 112.0903 Evaluate side-chains 120 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 1104 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 350 VAL 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 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 755 GLN 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 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 83 LEU 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: 2.9990 chunk 212 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 319 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 544 ASN B 564 GLN B1005 GLN B1011 GLN C 52 GLN C 239 GLN C 777 ASN C1002 GLN ** T 35 ASN ** 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 = 0.4468 r_free = 0.4468 target = 0.071906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.044595 restraints weight = 230398.859| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 7.67 r_work: 0.3208 rms_B_bonded: 6.51 restraints_weight: 2.0000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6689 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= 0.238 Angle : 0.768 19.824 43181 Z= 0.367 Chirality : 0.054 1.523 4987 Planarity : 0.005 0.063 5485 Dihedral : 6.921 57.664 5409 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 93.99 % Rotamer: Outliers : 1.63 % Allowed : 14.99 % Favored : 83.38 % 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: -0.79 (0.13), residues: 3812 helix: 2.25 (0.20), residues: 671 sheet: -0.65 (0.17), residues: 894 loop : -1.39 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 24 TYR 0.040 0.002 TYR A 369 PHE 0.045 0.002 PHE A 374 TRP 0.020 0.002 TRP S 47 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00513 (31562) covalent geometry : angle 0.73093 (42938) SS BOND : bond 0.00536 ( 42) SS BOND : angle 1.10934 ( 84) hydrogen bonds : bond 0.04296 ( 1143) hydrogen bonds : angle 5.98017 ( 3288) Misc. bond : bond 0.01265 ( 2) link_BETA1-4 : bond 0.00527 ( 7) link_BETA1-4 : angle 1.96209 ( 21) link_NAG-ASN : bond 0.00765 ( 46) link_NAG-ASN : angle 4.13221 ( 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 149 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 1.198 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 740 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.9022 (ppp) REVERT: B 754 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9126 (pt) REVERT: C 177 MET cc_start: -0.0155 (mtt) cc_final: -0.0489 (mtt) REVERT: C 265 TYR cc_start: 0.6334 (OUTLIER) cc_final: 0.6011 (p90) REVERT: C 560 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4563 (mt) REVERT: C 564 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8375 (tp-100) REVERT: C 697 MET cc_start: 0.9033 (ttm) cc_final: 0.8729 (mtm) REVERT: R 63 LYS cc_start: 0.7817 (pttm) cc_final: 0.7500 (pmtt) REVERT: S 81 MET cc_start: 0.8305 (ptm) cc_final: 0.7281 (ppp) REVERT: P 62 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8343 (ttt180) outliers start: 54 outliers final: 25 residues processed: 142 average time/residue: 0.6022 time to fit residues: 102.5714 Evaluate side-chains 123 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 213 VAL 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 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 560 LEU 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 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain T residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 48 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 258 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 chunk 264 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN B 564 GLN C 239 GLN C 493 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.071853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.044641 restraints weight = 228094.781| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 8.30 r_work: 0.3204 rms_B_bonded: 7.09 restraints_weight: 2.0000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31659 Z= 0.186 Angle : 0.723 17.670 43181 Z= 0.346 Chirality : 0.050 0.659 4987 Planarity : 0.004 0.062 5485 Dihedral : 6.568 56.618 5409 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 1.38 % Allowed : 15.35 % Favored : 83.26 % 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: 2.42 (0.20), residues: 668 sheet: -0.58 (0.17), residues: 871 loop : -1.36 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG T 87 TYR 0.034 0.001 TYR A 369 PHE 0.047 0.001 PHE A 374 TRP 0.024 0.002 TRP S 47 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00402 (31562) covalent geometry : angle 0.69076 (42938) SS BOND : bond 0.00389 ( 42) SS BOND : angle 0.94907 ( 84) hydrogen bonds : bond 0.04008 ( 1143) hydrogen bonds : angle 5.83150 ( 3288) Misc. bond : bond 0.01112 ( 2) link_BETA1-4 : bond 0.00564 ( 7) link_BETA1-4 : angle 1.88274 ( 21) link_NAG-ASN : bond 0.00570 ( 46) link_NAG-ASN : angle 3.74617 ( 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 145 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 1.013 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: 0.2954 (mpt) cc_final: 0.2601 (mpt) REVERT: B 350 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 740 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8923 (ppp) REVERT: B 754 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9131 (pp) REVERT: C 177 MET cc_start: 0.3857 (mtt) cc_final: 0.1780 (mtt) REVERT: C 265 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5882 (p90) REVERT: C 560 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5080 (mt) REVERT: C 564 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8599 (mm-40) REVERT: C 697 MET cc_start: 0.9066 (ttm) cc_final: 0.8837 (mtp) REVERT: C 755 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8024 (pp30) REVERT: S 48 MET cc_start: 0.7711 (pmm) cc_final: 0.7437 (pmm) REVERT: S 81 MET cc_start: 0.8412 (ptm) cc_final: 0.7412 (ppp) REVERT: T 46 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7873 (mp0) REVERT: T 48 MET cc_start: 0.7147 (pmm) cc_final: 0.6941 (pmm) outliers start: 46 outliers final: 27 residues processed: 138 average time/residue: 0.6081 time to fit residues: 101.1638 Evaluate side-chains 126 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU 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 51 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 119 ILE 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 560 LEU Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 62 ARG 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: 0.9980 chunk 5 optimal weight: 10.0000 chunk 369 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 362 optimal weight: 0.4980 chunk 370 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 564 GLN B1011 GLN C 196 ASN C 710 ASN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.071395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.044141 restraints weight = 229178.182| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 7.93 r_work: 0.3192 rms_B_bonded: 6.80 restraints_weight: 2.0000 r_work: 0.3285 rms_B_bonded: 5.05 restraints_weight: 4.0000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31659 Z= 0.188 Angle : 0.724 17.209 43181 Z= 0.348 Chirality : 0.050 0.597 4987 Planarity : 0.004 0.056 5485 Dihedral : 6.386 57.165 5409 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 1.32 % Allowed : 15.68 % Favored : 82.99 % 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: -0.63 (0.13), residues: 3812 helix: 2.50 (0.20), residues: 663 sheet: -0.51 (0.17), residues: 857 loop : -1.32 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 50 TYR 0.029 0.002 TYR C 505 PHE 0.049 0.002 PHE A 374 TRP 0.031 0.002 TRP C 104 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00406 (31562) covalent geometry : angle 0.69193 (42938) SS BOND : bond 0.00466 ( 42) SS BOND : angle 1.04953 ( 84) hydrogen bonds : bond 0.04018 ( 1143) hydrogen bonds : angle 5.75644 ( 3288) Misc. bond : bond 0.01043 ( 2) link_BETA1-4 : bond 0.00470 ( 7) link_BETA1-4 : angle 1.89761 ( 21) link_NAG-ASN : bond 0.00577 ( 46) link_NAG-ASN : angle 3.71549 ( 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 140 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 96 time to evaluate : 0.865 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: 0.2145 (mpt) cc_final: 0.1783 (mpt) REVERT: B 266 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: B 448 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8751 (m-40) REVERT: B 754 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9088 (pp) REVERT: C 63 THR cc_start: 0.6878 (m) cc_final: 0.6591 (t) REVERT: C 177 MET cc_start: 0.1743 (mtt) cc_final: 0.0620 (mtt) REVERT: C 265 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5907 (p90) REVERT: C 269 TYR cc_start: 0.5214 (OUTLIER) cc_final: 0.4796 (m-80) REVERT: C 560 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.5327 (mt) REVERT: C 697 MET cc_start: 0.8776 (ttm) cc_final: 0.8552 (mtp) REVERT: C 755 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7841 (pp30) REVERT: S 48 MET cc_start: 0.7573 (pmm) cc_final: 0.7287 (pmm) REVERT: S 81 MET cc_start: 0.8374 (ptm) cc_final: 0.7474 (ppp) REVERT: P 62 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8435 (ttt180) REVERT: T 46 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7892 (mp0) outliers start: 44 outliers final: 23 residues processed: 133 average time/residue: 0.5712 time to fit residues: 92.2964 Evaluate side-chains 124 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 448 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 51 THR 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 269 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 258 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 293 optimal weight: 0.8980 chunk 180 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** 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 = 0.4452 r_free = 0.4452 target = 0.071245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.044106 restraints weight = 228561.115| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 8.15 r_work: 0.3186 rms_B_bonded: 6.41 restraints_weight: 2.0000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.7551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31659 Z= 0.180 Angle : 0.729 18.726 43181 Z= 0.351 Chirality : 0.050 0.507 4987 Planarity : 0.004 0.055 5485 Dihedral : 6.322 56.844 5409 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 1.20 % Allowed : 15.71 % Favored : 83.08 % 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: -0.62 (0.14), residues: 3812 helix: 2.51 (0.20), residues: 670 sheet: -0.50 (0.17), residues: 867 loop : -1.35 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 87 TYR 0.042 0.001 TYR A 369 PHE 0.045 0.001 PHE A 374 TRP 0.038 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00392 (31562) covalent geometry : angle 0.69875 (42938) SS BOND : bond 0.00441 ( 42) SS BOND : angle 1.04621 ( 84) hydrogen bonds : bond 0.03917 ( 1143) hydrogen bonds : angle 5.71189 ( 3288) Misc. bond : bond 0.01057 ( 2) link_BETA1-4 : bond 0.00478 ( 7) link_BETA1-4 : angle 1.89003 ( 21) link_NAG-ASN : bond 0.00555 ( 46) link_NAG-ASN : angle 3.65558 ( 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 135 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.766 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: 0.1604 (mpt) cc_final: 0.1237 (mpt) REVERT: B 266 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: B 350 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 740 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8799 (ppp) REVERT: B 754 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9139 (pp) REVERT: C 63 THR cc_start: 0.6951 (m) cc_final: 0.6648 (t) REVERT: C 177 MET cc_start: 0.0926 (mtt) cc_final: -0.0067 (mtt) REVERT: C 265 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6198 (p90) REVERT: C 269 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.5161 (m-80) REVERT: C 755 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7951 (pp30) REVERT: R 81 MET cc_start: 0.2891 (mmm) cc_final: 0.2673 (mmm) REVERT: S 81 MET cc_start: 0.8394 (ptm) cc_final: 0.7526 (ppp) outliers start: 40 outliers final: 26 residues processed: 129 average time/residue: 0.6235 time to fit residues: 96.5180 Evaluate side-chains 123 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 201 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 350 VAL 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 740 MET 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 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain T residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 144 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 chunk 375 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 180 optimal weight: 0.4980 chunk 174 optimal weight: 0.7980 chunk 299 optimal weight: 2.9990 chunk 357 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.071001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.043768 restraints weight = 230102.343| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 7.81 r_work: 0.3182 rms_B_bonded: 6.57 restraints_weight: 2.0000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.7707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31659 Z= 0.194 Angle : 0.728 18.745 43181 Z= 0.350 Chirality : 0.050 0.501 4987 Planarity : 0.004 0.055 5485 Dihedral : 6.254 56.818 5409 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 1.05 % Allowed : 15.92 % Favored : 83.02 % 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: -0.63 (0.14), residues: 3812 helix: 2.49 (0.20), residues: 671 sheet: -0.52 (0.17), residues: 889 loop : -1.34 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 87 TYR 0.036 0.001 TYR A 369 PHE 0.046 0.002 PHE A 374 TRP 0.040 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00422 (31562) covalent geometry : angle 0.69711 (42938) SS BOND : bond 0.00444 ( 42) SS BOND : angle 1.07948 ( 84) hydrogen bonds : bond 0.03977 ( 1143) hydrogen bonds : angle 5.72763 ( 3288) Misc. bond : bond 0.01094 ( 2) link_BETA1-4 : bond 0.00565 ( 7) link_BETA1-4 : angle 1.82371 ( 21) link_NAG-ASN : bond 0.00549 ( 46) link_NAG-ASN : angle 3.64204 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21422.29 seconds wall clock time: 362 minutes 27.07 seconds (21747.07 seconds total)