Starting phenix.real_space_refine on Thu Jun 26 18:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a95_15270/06_2025/8a95_15270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a95_15270/06_2025/8a95_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_15270/06_2025/8a95_15270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a95_15270/06_2025/8a95_15270.map" model { file = "/net/cci-nas-00/data/ceres_data/8a95_15270/06_2025/8a95_15270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a95_15270/06_2025/8a95_15270.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 2.44s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.56, per 1000 atoms: 0.67 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: 7.66 Conformation dependent library (CDL) restraints added in 4.2 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: 4.64 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: 16.23 Time building geometry restraints manager: 9.18 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 1146 or resid 1301 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 1146 or resid 1301 through 1314)) selection = (chain 'C' and (resid 14 through 1146 or resid 1301 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: 14.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.260 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 77.230 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.230 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:16.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.240 ------------------------------------------------------------------------------- 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 : 7.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.042 0.004 TRP C 886 HIS 0.027 0.002 HIS C 66 PHE 0.254 0.005 PHE A 377 TYR 0.164 0.004 TYR S 108 ARG 0.039 0.002 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01330 ( 46) link_NAG-ASN : angle 5.49854 ( 138) link_BETA1-4 : bond 0.00834 ( 7) link_BETA1-4 : angle 3.02379 ( 21) hydrogen bonds : bond 0.17184 ( 1143) hydrogen bonds : angle 7.71308 ( 3288) SS BOND : bond 0.00851 ( 42) SS BOND : angle 2.10755 ( 84) covalent geometry : bond 0.01012 (31562) covalent geometry : angle 1.30298 (42938) Misc. bond : bond 0.13173 ( 2) *********************** 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 : 3.410 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: C 177 MET cc_start: -0.0382 (mtt) cc_final: -0.1307 (mpp) REVERT: Q 87 TYR cc_start: 0.5786 (m-80) cc_final: 0.5189 (m-10) REVERT: Q 97 ARG cc_start: 0.4468 (mtp180) cc_final: 0.4177 (mmt180) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 1.5575 time to fit residues: 488.1681 Evaluate side-chains 128 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 195 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 347 optimal weight: 8.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 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 544 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 777 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.093607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.077362 restraints weight = 217980.142| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 5.11 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 31659 Z= 0.219 Angle : 0.823 23.588 43181 Z= 0.399 Chirality : 0.055 0.839 4987 Planarity : 0.005 0.078 5485 Dihedral : 9.720 107.488 5409 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 1.23 % Allowed : 8.46 % Favored : 90.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3812 helix: 2.18 (0.20), residues: 680 sheet: 0.04 (0.17), residues: 871 loop : -1.21 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 113 HIS 0.007 0.001 HIS C 519 PHE 0.076 0.002 PHE A 377 TYR 0.043 0.002 TYR S 108 ARG 0.009 0.001 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00693 ( 46) link_NAG-ASN : angle 3.81875 ( 138) link_BETA1-4 : bond 0.00534 ( 7) link_BETA1-4 : angle 2.28972 ( 21) hydrogen bonds : bond 0.04389 ( 1143) hydrogen bonds : angle 6.05926 ( 3288) SS BOND : bond 0.00423 ( 42) SS BOND : angle 0.99148 ( 84) covalent geometry : bond 0.00469 (31562) covalent geometry : angle 0.79316 (42938) Misc. bond : bond 0.03238 ( 2) *********************** 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 180 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 3.249 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: 0.9059 (mp0) cc_final: 0.8783 (mp0) REVERT: B 505 TYR cc_start: 0.8648 (m-10) cc_final: 0.8327 (t80) REVERT: C 505 TYR cc_start: 0.9108 (m-80) cc_final: 0.8821 (t80) REVERT: R 54 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5136 (pmm) REVERT: S 81 MET cc_start: 0.6552 (ptm) cc_final: 0.5974 (ppp) outliers start: 41 outliers final: 10 residues processed: 161 average time/residue: 1.5284 time to fit residues: 293.4214 Evaluate side-chains 123 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 54 MET Chi-restraints excluded: chain O residue 50 TYR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 118 LEU 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 367 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 253 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 134 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 913 GLN A1088 HIS B 360 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B 764 ASN C 121 ASN C 388 ASN C 606 ASN C1088 HIS R 35 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.073466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.045955 restraints weight = 231564.058| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 7.82 r_work: 0.3245 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 31659 Z= 0.374 Angle : 0.967 17.103 43181 Z= 0.482 Chirality : 0.058 0.883 4987 Planarity : 0.006 0.099 5485 Dihedral : 8.927 92.888 5409 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.55 % Rotamer: Outliers : 2.68 % Allowed : 10.99 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 3812 helix: 1.39 (0.19), residues: 688 sheet: -0.59 (0.16), residues: 889 loop : -1.47 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP R 47 HIS 0.006 0.002 HIS C 146 PHE 0.039 0.003 PHE A 374 TYR 0.051 0.003 TYR O 50 ARG 0.015 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.01039 ( 46) link_NAG-ASN : angle 4.13846 ( 138) link_BETA1-4 : bond 0.00668 ( 7) link_BETA1-4 : angle 2.03867 ( 21) hydrogen bonds : bond 0.05789 ( 1143) hydrogen bonds : angle 6.69064 ( 3288) SS BOND : bond 0.00847 ( 42) SS BOND : angle 1.68259 ( 84) covalent geometry : bond 0.00806 (31562) covalent geometry : angle 0.93678 (42938) Misc. bond : bond 0.01693 ( 2) *********************** 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 210 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 121 time to evaluate : 3.526 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 134 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8837 (pm20) REVERT: A 198 ASP cc_start: 0.8995 (m-30) cc_final: 0.8681 (t70) REVERT: A 201 PHE cc_start: 0.8101 (t80) cc_final: 0.7669 (t80) REVERT: A 900 MET cc_start: 0.8814 (mmm) cc_final: 0.8389 (mtt) REVERT: B 63 THR cc_start: 0.8001 (m) cc_final: 0.7713 (p) REVERT: B 153 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9161 (mpm) REVERT: B 697 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8617 (ptm) REVERT: C 34 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.5297 (mmt180) REVERT: C 177 MET cc_start: 0.1337 (mpt) cc_final: 0.0978 (mpp) REVERT: C 200 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8459 (t80) REVERT: C 505 TYR cc_start: 0.9643 (m-80) cc_final: 0.9418 (t80) REVERT: C 564 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8184 (tp40) REVERT: R 54 MET cc_start: 0.8683 (mpp) cc_final: 0.8459 (pmm) REVERT: R 63 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6157 (pmtt) REVERT: P 62 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8586 (ptt-90) outliers start: 89 outliers final: 24 residues processed: 191 average time/residue: 1.2887 time to fit residues: 300.0798 Evaluate side-chains 130 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 3.704 ------------------------------------------------------------------------------- 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 204 TYR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 34 ARG 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 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 63 LYS Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 128 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 303 optimal weight: 0.8980 chunk 305 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 348 optimal weight: 30.0000 chunk 278 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 276 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 188 ASN A 913 GLN B 87 ASN B 564 GLN B 644 GLN C 239 GLN C1071 GLN R 35 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.074589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.047497 restraints weight = 228907.016| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 8.18 r_work: 0.3276 rms_B_bonded: 6.64 restraints_weight: 2.0000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 31659 Z= 0.149 Angle : 0.728 18.318 43181 Z= 0.351 Chirality : 0.052 0.843 4987 Planarity : 0.004 0.059 5485 Dihedral : 7.974 83.913 5409 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 2.14 % Allowed : 12.58 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 3812 helix: 2.07 (0.20), residues: 678 sheet: -0.36 (0.17), residues: 847 loop : -1.37 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.004 0.001 HIS B 66 PHE 0.047 0.002 PHE A 374 TYR 0.026 0.002 TYR S 108 ARG 0.012 0.001 ARG T 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 46) link_NAG-ASN : angle 3.64499 ( 138) link_BETA1-4 : bond 0.00502 ( 7) link_BETA1-4 : angle 2.03657 ( 21) hydrogen bonds : bond 0.04146 ( 1143) hydrogen bonds : angle 5.98509 ( 3288) SS BOND : bond 0.00346 ( 42) SS BOND : angle 0.94499 ( 84) covalent geometry : bond 0.00322 (31562) covalent geometry : angle 0.69796 (42938) Misc. bond : bond 0.01541 ( 2) *********************** 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 184 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 113 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.9122 (m-30) cc_final: 0.8771 (t70) REVERT: A 201 PHE cc_start: 0.8073 (t80) cc_final: 0.7759 (t80) REVERT: A 858 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9045 (pt) REVERT: A 988 GLU cc_start: 0.9625 (mp0) cc_final: 0.9416 (mp0) REVERT: B 63 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7627 (p) REVERT: B 244 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7267 (pt) REVERT: B 505 TYR cc_start: 0.9697 (OUTLIER) cc_final: 0.9333 (t80) REVERT: C 177 MET cc_start: 0.2388 (mpt) cc_final: 0.2022 (mpt) REVERT: C 564 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8070 (tp40) REVERT: R 48 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5247 (pmm) REVERT: R 54 MET cc_start: 0.8673 (mpp) cc_final: 0.8394 (pmm) REVERT: P 43 GLN cc_start: 0.9102 (tp40) cc_final: 0.8864 (tm-30) REVERT: T 91 THR cc_start: 0.9006 (p) cc_final: 0.8762 (m) REVERT: Q 90 GLN cc_start: -0.0801 (OUTLIER) cc_final: -0.1302 (tp40) outliers start: 71 outliers final: 18 residues processed: 168 average time/residue: 1.5767 time to fit residues: 325.2766 Evaluate side-chains 129 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 858 LEU 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 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR 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 552 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 55 PHE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 105 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A1005 GLN B1005 GLN C 146 HIS C 239 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.074103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.046794 restraints weight = 228182.865| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 8.23 r_work: 0.3269 rms_B_bonded: 6.61 restraints_weight: 2.0000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31659 Z= 0.160 Angle : 0.708 17.237 43181 Z= 0.339 Chirality : 0.050 0.659 4987 Planarity : 0.004 0.051 5485 Dihedral : 7.235 65.746 5409 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 1.87 % Allowed : 13.31 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3812 helix: 2.32 (0.20), residues: 676 sheet: -0.34 (0.17), residues: 833 loop : -1.29 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.004 0.001 HIS C 519 PHE 0.046 0.001 PHE A 374 TYR 0.056 0.002 TYR A 369 ARG 0.006 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 46) link_NAG-ASN : angle 3.65073 ( 138) link_BETA1-4 : bond 0.00534 ( 7) link_BETA1-4 : angle 2.02726 ( 21) hydrogen bonds : bond 0.03992 ( 1143) hydrogen bonds : angle 5.78584 ( 3288) SS BOND : bond 0.00362 ( 42) SS BOND : angle 0.94655 ( 84) covalent geometry : bond 0.00345 (31562) covalent geometry : angle 0.67643 (42938) Misc. bond : bond 0.01258 ( 2) *********************** 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 176 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 114 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.9005 (m-30) cc_final: 0.8666 (t70) REVERT: A 201 PHE cc_start: 0.8017 (t80) cc_final: 0.7677 (t80) REVERT: A 858 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9121 (pt) REVERT: A 988 GLU cc_start: 0.9613 (mp0) cc_final: 0.9379 (mp0) REVERT: B 63 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7840 (p) REVERT: B 505 TYR cc_start: 0.9612 (OUTLIER) cc_final: 0.9198 (t80) REVERT: C 177 MET cc_start: 0.2230 (mpt) cc_final: 0.1772 (mpt) REVERT: C 455 LEU cc_start: 0.9669 (tm) cc_final: 0.9461 (pt) REVERT: C 456 PHE cc_start: 0.8964 (m-80) cc_final: 0.8710 (m-80) REVERT: C 564 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8096 (tp-100) REVERT: P 50 TYR cc_start: 0.9545 (p90) cc_final: 0.9319 (p90) REVERT: P 62 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8400 (ttt180) REVERT: T 81 MET cc_start: 0.2096 (mmm) cc_final: 0.1807 (mmm) REVERT: Q 90 GLN cc_start: -0.1943 (OUTLIER) cc_final: -0.2687 (tp40) outliers start: 62 outliers final: 24 residues processed: 166 average time/residue: 1.2760 time to fit residues: 257.5958 Evaluate side-chains 133 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 3.164 ------------------------------------------------------------------------------- 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 374 PHE Chi-restraints excluded: chain A residue 858 LEU 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 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 30 ASN Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain Q residue 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 110 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 339 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 210 optimal weight: 0.3980 chunk 235 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN B1005 GLN C 239 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.074331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.047081 restraints weight = 227527.344| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 8.26 r_work: 0.3266 rms_B_bonded: 6.84 restraints_weight: 2.0000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31659 Z= 0.133 Angle : 0.694 16.820 43181 Z= 0.329 Chirality : 0.050 0.554 4987 Planarity : 0.004 0.050 5485 Dihedral : 6.787 58.130 5409 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.02 % Rotamer: Outliers : 1.48 % Allowed : 14.48 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3812 helix: 2.37 (0.20), residues: 682 sheet: -0.30 (0.17), residues: 821 loop : -1.27 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.004 0.001 HIS C 49 PHE 0.046 0.001 PHE A 374 TYR 0.052 0.001 TYR A 369 ARG 0.007 0.000 ARG R 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 46) link_NAG-ASN : angle 3.55626 ( 138) link_BETA1-4 : bond 0.00527 ( 7) link_BETA1-4 : angle 2.00350 ( 21) hydrogen bonds : bond 0.03770 ( 1143) hydrogen bonds : angle 5.58414 ( 3288) SS BOND : bond 0.00288 ( 42) SS BOND : angle 0.78958 ( 84) covalent geometry : bond 0.00285 (31562) covalent geometry : angle 0.66386 (42938) Misc. bond : bond 0.01160 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.9032 (m-30) cc_final: 0.8640 (t70) REVERT: A 201 PHE cc_start: 0.8009 (t80) cc_final: 0.7687 (t80) REVERT: A 988 GLU cc_start: 0.9614 (mp0) cc_final: 0.9316 (mp0) REVERT: B 63 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 244 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7566 (pt) REVERT: C 177 MET cc_start: 0.2801 (mpt) cc_final: 0.2050 (mpt) REVERT: C 564 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8250 (tp-100) REVERT: C 697 MET cc_start: 0.9038 (ttm) cc_final: 0.8555 (mtm) REVERT: R 48 MET cc_start: 0.6809 (mpt) cc_final: 0.6552 (mpp) REVERT: P 50 TYR cc_start: 0.9559 (p90) cc_final: 0.9345 (p90) REVERT: T 81 MET cc_start: 0.2680 (mmm) cc_final: 0.2173 (mmm) REVERT: Q 90 GLN cc_start: -0.3155 (OUTLIER) cc_final: -0.3952 (tp40) outliers start: 49 outliers final: 20 residues processed: 148 average time/residue: 1.3608 time to fit residues: 246.2658 Evaluate side-chains 121 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 3.506 ------------------------------------------------------------------------------- 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 374 PHE Chi-restraints excluded: chain A residue 705 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 244 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 791 THR 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 244 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain T residue 29 PHE Chi-restraints excluded: chain Q residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 322 optimal weight: 8.9990 chunk 359 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN B1011 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 777 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.072240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.044611 restraints weight = 229141.327| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 8.26 r_work: 0.3204 rms_B_bonded: 7.25 restraints_weight: 2.0000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 31659 Z= 0.261 Angle : 0.764 16.815 43181 Z= 0.371 Chirality : 0.050 0.550 4987 Planarity : 0.005 0.170 5485 Dihedral : 6.776 57.840 5409 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.89 % Rotamer: Outliers : 1.84 % Allowed : 14.63 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3812 helix: 2.36 (0.20), residues: 669 sheet: -0.58 (0.17), residues: 877 loop : -1.33 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 47 HIS 0.004 0.001 HIS B 66 PHE 0.041 0.002 PHE A 374 TYR 0.032 0.002 TYR A 369 ARG 0.012 0.001 ARG T 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 46) link_NAG-ASN : angle 3.63885 ( 138) link_BETA1-4 : bond 0.00517 ( 7) link_BETA1-4 : angle 1.96523 ( 21) hydrogen bonds : bond 0.04358 ( 1143) hydrogen bonds : angle 5.89263 ( 3288) SS BOND : bond 0.00578 ( 42) SS BOND : angle 1.10387 ( 84) covalent geometry : bond 0.00562 (31562) covalent geometry : angle 0.73487 (42938) Misc. bond : bond 0.01270 ( 2) *********************** 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 164 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 103 time to evaluate : 3.265 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: 0.2839 (mpt) cc_final: 0.2384 (mpt) REVERT: A 198 ASP cc_start: 0.9354 (m-30) cc_final: 0.8824 (t70) REVERT: A 988 GLU cc_start: 0.9630 (mp0) cc_final: 0.9374 (mp0) REVERT: B 63 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7623 (t) REVERT: B 350 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8937 (p) REVERT: C 15 CYS cc_start: 0.7582 (OUTLIER) cc_final: 0.5905 (t) REVERT: C 177 MET cc_start: 0.4965 (mpt) cc_final: 0.3706 (mpt) REVERT: C 564 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8610 (tp-100) REVERT: R 48 MET cc_start: 0.6831 (mpt) cc_final: 0.6623 (mpp) REVERT: R 86 LEU cc_start: 0.1146 (OUTLIER) cc_final: -0.0275 (tt) REVERT: S 48 MET cc_start: 0.7609 (pmm) cc_final: 0.7407 (pmm) REVERT: S 81 MET cc_start: 0.8180 (mtt) cc_final: 0.7621 (mmt) REVERT: P 50 TYR cc_start: 0.9604 (p90) cc_final: 0.9403 (p90) outliers start: 61 outliers final: 29 residues processed: 159 average time/residue: 1.2528 time to fit residues: 244.2929 Evaluate side-chains 128 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 3.563 ------------------------------------------------------------------------------- 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 374 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU 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 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain T residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 300 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 362 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 364 optimal weight: 20.0000 chunk 267 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN C 239 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.073097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.045900 restraints weight = 229000.824| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 8.18 r_work: 0.3238 rms_B_bonded: 6.33 restraints_weight: 2.0000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31659 Z= 0.141 Angle : 0.698 15.775 43181 Z= 0.332 Chirality : 0.050 0.503 4987 Planarity : 0.004 0.050 5485 Dihedral : 6.497 56.506 5409 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 1.17 % Allowed : 15.92 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3812 helix: 2.55 (0.20), residues: 666 sheet: -0.45 (0.17), residues: 850 loop : -1.27 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.005 0.001 HIS C 49 PHE 0.039 0.001 PHE A 374 TYR 0.034 0.001 TYR A 369 ARG 0.005 0.000 ARG P 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 46) link_NAG-ASN : angle 3.48296 ( 138) link_BETA1-4 : bond 0.00414 ( 7) link_BETA1-4 : angle 1.96071 ( 21) hydrogen bonds : bond 0.03791 ( 1143) hydrogen bonds : angle 5.63108 ( 3288) SS BOND : bond 0.00320 ( 42) SS BOND : angle 0.82462 ( 84) covalent geometry : bond 0.00305 (31562) covalent geometry : angle 0.66906 (42938) Misc. bond : bond 0.01131 ( 2) *********************** 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 136 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 3.932 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: 0.0966 (mpt) cc_final: 0.0618 (mpt) REVERT: A 198 ASP cc_start: 0.9316 (m-30) cc_final: 0.8852 (t70) REVERT: A 900 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7777 (mmm) REVERT: B 63 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7734 (t) REVERT: B 244 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7537 (pt) REVERT: B 350 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8930 (p) REVERT: B 740 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8903 (ppp) REVERT: B 773 GLU cc_start: 0.8841 (tp30) cc_final: 0.8397 (tp30) REVERT: C 177 MET cc_start: 0.2983 (mpt) cc_final: 0.2046 (mpt) REVERT: C 490 PHE cc_start: 0.8927 (t80) cc_final: 0.8636 (t80) REVERT: C 564 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8439 (tp-100) REVERT: C 697 MET cc_start: 0.9056 (ttm) cc_final: 0.8760 (mtm) REVERT: O 59 ILE cc_start: 0.5993 (OUTLIER) cc_final: 0.5234 (pt) REVERT: S 48 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7592 (pmm) REVERT: S 81 MET cc_start: 0.8020 (mtt) cc_final: 0.7376 (mmt) outliers start: 39 outliers final: 25 residues processed: 129 average time/residue: 1.9393 time to fit residues: 311.4363 Evaluate side-chains 123 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 4.108 ------------------------------------------------------------------------------- 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 374 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 898 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU 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 740 MET Chi-restraints excluded: chain B residue 791 THR 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 244 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain T residue 54 MET 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 342 optimal weight: 20.0000 chunk 262 optimal weight: 0.6980 chunk 329 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 274 optimal weight: 0.5980 chunk 354 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN B 544 ASN B 564 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.072562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.045362 restraints weight = 227700.260| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 8.24 r_work: 0.3215 rms_B_bonded: 6.60 restraints_weight: 2.0000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31659 Z= 0.159 Angle : 0.699 15.276 43181 Z= 0.335 Chirality : 0.049 0.508 4987 Planarity : 0.004 0.051 5485 Dihedral : 6.229 56.816 5409 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 1.26 % Allowed : 16.01 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3812 helix: 2.60 (0.20), residues: 668 sheet: -0.50 (0.17), residues: 869 loop : -1.24 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 104 HIS 0.004 0.001 HIS C 49 PHE 0.033 0.001 PHE A 374 TYR 0.029 0.002 TYR A 369 ARG 0.004 0.000 ARG R 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 46) link_NAG-ASN : angle 3.45310 ( 138) link_BETA1-4 : bond 0.00512 ( 7) link_BETA1-4 : angle 1.93610 ( 21) hydrogen bonds : bond 0.03811 ( 1143) hydrogen bonds : angle 5.54130 ( 3288) SS BOND : bond 0.00375 ( 42) SS BOND : angle 0.87024 ( 84) covalent geometry : bond 0.00348 (31562) covalent geometry : angle 0.67108 (42938) Misc. bond : bond 0.01033 ( 2) *********************** 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 136 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 3.370 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: 0.0462 (mpt) cc_final: 0.0128 (mpt) REVERT: A 198 ASP cc_start: 0.9329 (m-30) cc_final: 0.8828 (t70) REVERT: B 63 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7785 (t) REVERT: B 740 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8943 (ppp) REVERT: B 773 GLU cc_start: 0.8858 (tp30) cc_final: 0.8369 (tp30) REVERT: C 177 MET cc_start: 0.2891 (mpt) cc_final: 0.2061 (mpt) REVERT: C 564 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8568 (tp40) REVERT: C 697 MET cc_start: 0.9034 (ttm) cc_final: 0.8620 (mtm) REVERT: S 48 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7449 (pmm) REVERT: S 81 MET cc_start: 0.8096 (mtt) cc_final: 0.7505 (mmt) outliers start: 42 outliers final: 25 residues processed: 130 average time/residue: 1.1902 time to fit residues: 192.5262 Evaluate side-chains 113 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 3.689 ------------------------------------------------------------------------------- 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 374 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU 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 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 28 TYR 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 244 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 48 MET Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 97 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 363 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.071006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.043589 restraints weight = 230072.561| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 7.95 r_work: 0.3166 rms_B_bonded: 7.05 restraints_weight: 2.0000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.7611 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= 0.243 Angle : 0.775 14.212 43181 Z= 0.376 Chirality : 0.051 0.510 4987 Planarity : 0.005 0.108 5485 Dihedral : 6.547 56.783 5409 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 1.05 % Allowed : 16.29 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 3812 helix: 2.43 (0.20), residues: 677 sheet: -0.61 (0.17), residues: 860 loop : -1.36 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 104 HIS 0.004 0.001 HIS B 66 PHE 0.031 0.002 PHE A 377 TYR 0.052 0.002 TYR A 369 ARG 0.013 0.001 ARG T 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 46) link_NAG-ASN : angle 3.53288 ( 138) link_BETA1-4 : bond 0.00520 ( 7) link_BETA1-4 : angle 1.84780 ( 21) hydrogen bonds : bond 0.04291 ( 1143) hydrogen bonds : angle 5.88479 ( 3288) SS BOND : bond 0.00607 ( 42) SS BOND : angle 1.27174 ( 84) covalent geometry : bond 0.00525 (31562) covalent geometry : angle 0.74779 (42938) Misc. bond : bond 0.00966 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 3.539 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 111 ASP cc_start: 0.9288 (m-30) cc_final: 0.9064 (p0) REVERT: A 177 MET cc_start: 0.3350 (mpt) cc_final: 0.2812 (mpt) REVERT: A 198 ASP cc_start: 0.9632 (m-30) cc_final: 0.9139 (t0) REVERT: B 63 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 740 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8975 (ppp) REVERT: B 754 LEU cc_start: 0.9399 (mm) cc_final: 0.9115 (pp) REVERT: C 63 THR cc_start: 0.6782 (m) cc_final: 0.6538 (t) REVERT: C 177 MET cc_start: 0.5923 (mpt) cc_final: 0.4525 (mpt) REVERT: C 564 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8080 (tm-30) REVERT: C 697 MET cc_start: 0.9073 (ttm) cc_final: 0.8564 (mtm) REVERT: S 48 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7385 (pmm) REVERT: S 54 MET cc_start: 0.9436 (ppp) cc_final: 0.9031 (ppp) REVERT: S 81 MET cc_start: 0.8105 (mtt) cc_final: 0.7460 (mmt) REVERT: P 24 ARG cc_start: 0.9802 (tpp80) cc_final: 0.9557 (mpp80) outliers start: 35 outliers final: 21 residues processed: 125 average time/residue: 1.3617 time to fit residues: 210.4788 Evaluate side-chains 114 residues out of total 3343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 3.354 ------------------------------------------------------------------------------- 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 374 PHE Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 976 VAL 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 244 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 48 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 340 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 202 optimal weight: 0.4980 chunk 368 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 378 optimal weight: 30.0000 chunk 219 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** O 90 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.071358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.043761 restraints weight = 229043.684| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 8.28 r_work: 0.3197 rms_B_bonded: 7.13 restraints_weight: 2.0000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31659 Z= 0.167 Angle : 0.709 15.887 43181 Z= 0.340 Chirality : 0.049 0.498 4987 Planarity : 0.004 0.051 5485 Dihedral : 6.177 56.387 5409 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.84 % Allowed : 16.65 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3812 helix: 2.59 (0.20), residues: 671 sheet: -0.52 (0.17), residues: 864 loop : -1.33 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 104 HIS 0.005 0.001 HIS B 66 PHE 0.028 0.001 PHE A 374 TYR 0.047 0.001 TYR A 369 ARG 0.008 0.000 ARG R 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 46) link_NAG-ASN : angle 3.48536 ( 138) link_BETA1-4 : bond 0.00499 ( 7) link_BETA1-4 : angle 1.82509 ( 21) hydrogen bonds : bond 0.03843 ( 1143) hydrogen bonds : angle 5.67496 ( 3288) SS BOND : bond 0.00389 ( 42) SS BOND : angle 0.99266 ( 84) covalent geometry : bond 0.00362 (31562) covalent geometry : angle 0.68020 (42938) Misc. bond : bond 0.01226 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43277.42 seconds wall clock time: 738 minutes 39.96 seconds (44319.96 seconds total)