Starting phenix.real_space_refine on Fri Jun 27 01:32:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zr9_14887/06_2025/7zr9_14887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zr9_14887/06_2025/7zr9_14887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zr9_14887/06_2025/7zr9_14887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zr9_14887/06_2025/7zr9_14887.map" model { file = "/net/cci-nas-00/data/ceres_data/7zr9_14887/06_2025/7zr9_14887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zr9_14887/06_2025/7zr9_14887.cif" } resolution = 4.0 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= 0.080 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 141 5.16 5 C 19719 2.51 5 N 5108 2.21 5 O 6046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31014 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.90, per 1000 atoms: 0.54 Number of scatterers: 31014 At special positions: 0 Unit cell: (153.6, 163.2, 232.8, 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 141 16.00 O 6046 8.00 N 5108 7.00 C 19719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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 288 " - pdb=" SG CYS B 298 " distance=2.02 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 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 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 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 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=1.67 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 105 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 105 " distance=2.21 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 105 " distance=2.21 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 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=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 600 " " NAG C1305 " - " ASN C 613 " " NAG C1306 " - " ASN C 654 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 340 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN A 714 " " NAG O 1 " - " ASN A 798 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 3.7 seconds 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7234 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 69 sheets defined 22.2% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.636A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.693A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.217A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.575A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.745A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.544A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.161A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.616A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.427A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.132A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.525A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.768A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.951A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 4.066A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.594A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 5.051A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.885A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 382 through 387 removed outlier: 3.735A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.572A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.809A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 938 removed outlier: 5.599A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.958A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.927A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.992A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 56 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.639A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.533A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.748A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.133A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.475A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.807A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.509A pdb=" N ALA B 691 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AB6, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.931A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.659A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.448A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AC3, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AC4, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.974A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.388A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.885A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 151 through 160 removed outlier: 6.834A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.195A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AD1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AD2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.915A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD4, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.511A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.503A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.700A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.700A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AD9, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.874A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 3.567A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.859A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.009A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.398A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.230A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 141 " --> pdb=" O HIS C 242 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.608A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.313A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.244A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.863A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.557A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.841A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.366A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 3.747A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR E 70 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N GLN E 27 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER E 68 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.582A pdb=" N VAL E 29 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N SER E 66 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.631A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AH2, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR G 70 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLN G 27 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER G 68 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL G 29 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N SER G 66 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.630A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 1319 hydrogen bonds defined for protein. 3480 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: 15.13 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9769 1.34 - 1.46: 7184 1.46 - 1.58: 14598 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 31731 Sorted by residual: bond pdb=" CA TRP D 121 " pdb=" C TRP D 121 " ideal model delta sigma weight residual 1.520 1.398 0.121 1.16e-02 7.43e+03 1.10e+02 bond pdb=" CA TRP H 121 " pdb=" C TRP H 121 " ideal model delta sigma weight residual 1.520 1.399 0.121 1.16e-02 7.43e+03 1.09e+02 bond pdb=" CA TRP F 121 " pdb=" C TRP F 121 " ideal model delta sigma weight residual 1.520 1.399 0.121 1.16e-02 7.43e+03 1.08e+02 bond pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.51e-02 4.39e+03 1.96e+01 bond pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.51e-02 4.39e+03 1.94e+01 ... (remaining 31726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 42688 3.10 - 6.21: 449 6.21 - 9.31: 30 9.31 - 12.41: 7 12.41 - 15.52: 6 Bond angle restraints: 43180 Sorted by residual: angle pdb=" C CYS H 105 " pdb=" N PRO H 106 " pdb=" CA PRO H 106 " ideal model delta sigma weight residual 119.84 109.93 9.91 1.25e+00 6.40e-01 6.29e+01 angle pdb=" C CYS D 105 " pdb=" N PRO D 106 " pdb=" CA PRO D 106 " ideal model delta sigma weight residual 119.84 109.95 9.89 1.25e+00 6.40e-01 6.26e+01 angle pdb=" C CYS F 105 " pdb=" N PRO F 106 " pdb=" CA PRO F 106 " ideal model delta sigma weight residual 119.84 109.96 9.88 1.25e+00 6.40e-01 6.25e+01 angle pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " pdb=" SG CYS D 101 " ideal model delta sigma weight residual 114.40 98.88 15.52 2.30e+00 1.89e-01 4.55e+01 angle pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " ideal model delta sigma weight residual 114.40 98.90 15.50 2.30e+00 1.89e-01 4.54e+01 ... (remaining 43175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 18518 17.85 - 35.71: 810 35.71 - 53.56: 162 53.56 - 71.41: 42 71.41 - 89.26: 18 Dihedral angle restraints: 19550 sinusoidal: 8264 harmonic: 11286 Sorted by residual: dihedral pdb=" C CYS D 101 " pdb=" N CYS D 101 " pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " ideal model delta harmonic sigma weight residual -122.60 -109.26 -13.34 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C CYS H 101 " pdb=" N CYS H 101 " pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " ideal model delta harmonic sigma weight residual -122.60 -109.26 -13.34 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C CYS F 101 " pdb=" N CYS F 101 " pdb=" CA CYS F 101 " pdb=" CB CYS F 101 " ideal model delta harmonic sigma weight residual -122.60 -109.33 -13.27 0 2.50e+00 1.60e-01 2.82e+01 ... (remaining 19547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3586 0.046 - 0.091: 909 0.091 - 0.137: 414 0.137 - 0.183: 81 0.183 - 0.229: 25 Chirality restraints: 5015 Sorted by residual: chirality pdb=" CA PRO H 53 " pdb=" N PRO H 53 " pdb=" C PRO H 53 " pdb=" CB PRO H 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO F 53 " pdb=" N PRO F 53 " pdb=" C PRO F 53 " pdb=" CB PRO F 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO D 53 " pdb=" N PRO D 53 " pdb=" C PRO D 53 " pdb=" CB PRO D 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5012 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.240 2.00e-02 2.50e+03 2.01e-01 5.03e+02 pdb=" C7 NAG B1308 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.335 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " 0.058 2.00e-02 2.50e+03 3.51e-02 3.08e+01 pdb=" CG TRP L 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " -0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 36 " -0.058 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP E 36 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP E 36 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP E 36 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP E 36 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 36 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP E 36 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 36 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 36 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 36 " -0.054 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 958 2.71 - 3.25: 30537 3.25 - 3.80: 50386 3.80 - 4.35: 63216 4.35 - 4.90: 106475 Nonbonded interactions: 251572 Sorted by model distance: nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.158 3.040 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.172 3.040 nonbonded pdb=" O GLU B 306 " pdb=" OH TYR B 310 " model vdw 2.174 3.040 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN C 99 " pdb=" NH2 ARG C 190 " model vdw 2.178 3.120 ... (remaining 251567 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 13 through 619 or resid 638 through 1144 or resid 1301 thr \ ough 1310)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 619 or resid 638 through 1144 or resid 1301 thr \ ough 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 69.690 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.007 0.365 31836 Z= 0.379 Angle : 0.908 46.727 43444 Z= 0.525 Chirality : 0.052 0.229 5015 Planarity : 0.006 0.201 5513 Dihedral : 10.861 89.264 12163 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 1.22 % Allowed : 4.90 % Favored : 93.88 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.99 % 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: -0.10 (0.13), residues: 3845 helix: 1.21 (0.20), residues: 706 sheet: 0.16 (0.15), residues: 1043 loop : -0.59 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.006 TRP L 36 HIS 0.006 0.001 HIS B1045 PHE 0.032 0.002 PHE D 64 TYR 0.041 0.003 TYR F 94 ARG 0.014 0.001 ARG G 55 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 42) link_NAG-ASN : angle 1.87812 ( 126) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.00810 ( 36) hydrogen bonds : bond 0.13466 ( 1272) hydrogen bonds : angle 7.13014 ( 3480) SS BOND : bond 0.06648 ( 51) SS BOND : angle 5.51113 ( 102) covalent geometry : bond 0.00636 (31731) covalent geometry : angle 0.86437 (43180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 PHE cc_start: 0.5455 (m-80) cc_final: 0.5008 (m-10) REVERT: B 177 MET cc_start: 0.0753 (ttm) cc_final: 0.0388 (ttp) REVERT: B 239 GLN cc_start: 0.7634 (tt0) cc_final: 0.7408 (tt0) REVERT: B 267 LEU cc_start: 0.8901 (mt) cc_final: 0.8598 (mp) REVERT: B 284 ASP cc_start: 0.7423 (t0) cc_final: 0.6945 (t0) REVERT: B 612 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 760 LEU cc_start: 0.9542 (mt) cc_final: 0.9300 (mt) REVERT: A 54 LEU cc_start: 0.8996 (mt) cc_final: 0.8622 (mm) REVERT: A 65 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: A 104 TRP cc_start: 0.7425 (m-90) cc_final: 0.7199 (m-90) REVERT: A 118 LEU cc_start: 0.8355 (tp) cc_final: 0.7741 (mp) REVERT: A 133 PHE cc_start: 0.6574 (m-80) cc_final: 0.4814 (m-80) REVERT: A 177 MET cc_start: 0.3712 (ttm) cc_final: 0.2445 (mtp) REVERT: A 221 SER cc_start: 0.7487 (t) cc_final: 0.7143 (m) REVERT: A 1139 GLN cc_start: 0.8813 (tp40) cc_final: 0.8469 (tm-30) REVERT: C 87 ASN cc_start: 0.8432 (m-40) cc_final: 0.7585 (m110) REVERT: C 143 VAL cc_start: 0.4888 (OUTLIER) cc_final: 0.4677 (p) REVERT: C 177 MET cc_start: 0.0661 (ttm) cc_final: -0.2168 (mmt) REVERT: C 263 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: C 266 TYR cc_start: 0.7389 (m-80) cc_final: 0.7176 (m-10) REVERT: C 717 ILE cc_start: 0.9016 (mm) cc_final: 0.8811 (tt) REVERT: C 893 ILE cc_start: 0.9563 (OUTLIER) cc_final: 0.9215 (mt) REVERT: C 1020 ASN cc_start: 0.8699 (m-40) cc_final: 0.7381 (m-40) REVERT: H 81 MET cc_start: 0.4206 (tmm) cc_final: 0.3753 (ptt) REVERT: L 49 ILE cc_start: 0.7689 (mm) cc_final: 0.6809 (mm) REVERT: L 88 TYR cc_start: 0.1343 (m-80) cc_final: 0.1081 (m-80) REVERT: E 98 THR cc_start: 0.5772 (p) cc_final: 0.5217 (t) REVERT: G 4 MET cc_start: 0.4329 (mmm) cc_final: 0.3699 (mtt) outliers start: 41 outliers final: 12 residues processed: 416 average time/residue: 0.4292 time to fit residues: 287.3721 Evaluate side-chains 190 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 2.9990 chunk 293 optimal weight: 0.1980 chunk 162 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 303 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 351 optimal weight: 50.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 752 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.122143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.089910 restraints weight = 166472.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.087044 restraints weight = 138922.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.087268 restraints weight = 141176.224| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 31836 Z= 0.209 Angle : 0.616 8.623 43444 Z= 0.321 Chirality : 0.044 0.204 5015 Planarity : 0.004 0.090 5513 Dihedral : 6.750 59.773 5360 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 1.97 % Allowed : 9.10 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.08 (0.13), residues: 3845 helix: 1.44 (0.19), residues: 704 sheet: 0.12 (0.15), residues: 1040 loop : -0.42 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 883 HIS 0.006 0.001 HIS B1045 PHE 0.022 0.002 PHE A 135 TYR 0.034 0.001 TYR A 266 ARG 0.007 0.000 ARG C 574 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 42) link_NAG-ASN : angle 2.04862 ( 126) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 1.14532 ( 36) hydrogen bonds : bond 0.04493 ( 1272) hydrogen bonds : angle 5.90526 ( 3480) SS BOND : bond 0.00451 ( 51) SS BOND : angle 1.33002 ( 102) covalent geometry : bond 0.00457 (31731) covalent geometry : angle 0.60386 (43180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 PHE cc_start: 0.5330 (m-80) cc_final: 0.5044 (m-10) REVERT: B 177 MET cc_start: 0.2621 (ttm) cc_final: 0.2346 (ttp) REVERT: B 267 LEU cc_start: 0.9095 (mt) cc_final: 0.8775 (mp) REVERT: B 384 LEU cc_start: 0.8326 (mt) cc_final: 0.7798 (mt) REVERT: B 420 TYR cc_start: 0.5105 (t80) cc_final: 0.4482 (t80) REVERT: B 612 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8358 (p) REVERT: B 696 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7813 (mt) REVERT: A 65 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: A 87 ASN cc_start: 0.8865 (t0) cc_final: 0.8449 (t0) REVERT: A 177 MET cc_start: 0.4707 (ttm) cc_final: 0.4008 (mtp) REVERT: C 87 ASN cc_start: 0.8671 (m-40) cc_final: 0.7619 (m110) REVERT: C 118 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7953 (mt) REVERT: C 177 MET cc_start: 0.2545 (ttm) cc_final: -0.0442 (tpp) REVERT: C 203 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8756 (pt) REVERT: C 263 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.5839 (m-80) REVERT: C 266 TYR cc_start: 0.7536 (m-80) cc_final: 0.7261 (m-10) REVERT: C 899 MET cc_start: 0.9078 (tpp) cc_final: 0.8779 (tpp) REVERT: C 959 LEU cc_start: 0.9496 (tp) cc_final: 0.9295 (tp) REVERT: H 81 MET cc_start: 0.4737 (tmm) cc_final: 0.3697 (ptt) REVERT: D 47 TRP cc_start: 0.2089 (t60) cc_final: 0.0554 (t60) REVERT: D 48 MET cc_start: 0.2159 (OUTLIER) cc_final: 0.0878 (ptp) REVERT: E 4 MET cc_start: 0.4468 (mmt) cc_final: 0.4174 (mmt) REVERT: G 4 MET cc_start: 0.4124 (mmm) cc_final: 0.3784 (mtt) outliers start: 66 outliers final: 36 residues processed: 239 average time/residue: 0.4151 time to fit residues: 164.7100 Evaluate side-chains 173 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 50 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 245 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 302 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.121870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089935 restraints weight = 167199.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.088323 restraints weight = 133594.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.088471 restraints weight = 111380.648| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31836 Z= 0.173 Angle : 0.578 12.185 43444 Z= 0.296 Chirality : 0.044 0.296 5015 Planarity : 0.004 0.069 5513 Dihedral : 6.087 59.698 5350 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 2.69 % Allowed : 9.76 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.20 (0.14), residues: 3845 helix: 1.74 (0.20), residues: 711 sheet: 0.12 (0.15), residues: 1076 loop : -0.38 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 104 HIS 0.006 0.001 HIS B1045 PHE 0.023 0.002 PHE A 140 TYR 0.022 0.001 TYR A 266 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 42) link_NAG-ASN : angle 1.94994 ( 126) link_BETA1-4 : bond 0.00253 ( 12) link_BETA1-4 : angle 1.08028 ( 36) hydrogen bonds : bond 0.03983 ( 1272) hydrogen bonds : angle 5.59960 ( 3480) SS BOND : bond 0.00413 ( 51) SS BOND : angle 1.44371 ( 102) covalent geometry : bond 0.00380 (31731) covalent geometry : angle 0.56464 (43180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 151 time to evaluate : 3.236 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: B 33 THR cc_start: 0.9202 (p) cc_final: 0.8914 (t) REVERT: B 177 MET cc_start: 0.0873 (ttm) cc_final: 0.0587 (ttt) REVERT: B 267 LEU cc_start: 0.9105 (mt) cc_final: 0.8767 (mp) REVERT: B 420 TYR cc_start: 0.4845 (t80) cc_final: 0.4291 (t80) REVERT: B 612 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8392 (p) REVERT: B 696 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7841 (mt) REVERT: B 855 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 65 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: A 153 MET cc_start: 0.5069 (mmt) cc_final: 0.4802 (mmt) REVERT: A 177 MET cc_start: 0.3775 (ttm) cc_final: 0.2959 (mtp) REVERT: A 966 ASN cc_start: 0.8877 (m-40) cc_final: 0.8672 (m-40) REVERT: A 985 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: C 24 LEU cc_start: 0.1184 (OUTLIER) cc_final: 0.0777 (tp) REVERT: C 87 ASN cc_start: 0.8620 (m-40) cc_final: 0.8368 (m110) REVERT: C 118 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8000 (mt) REVERT: C 177 MET cc_start: 0.1310 (ttm) cc_final: -0.1687 (tpp) REVERT: C 263 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.5704 (m-80) REVERT: C 311 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: C 899 MET cc_start: 0.9114 (tpp) cc_final: 0.8809 (tpp) REVERT: C 959 LEU cc_start: 0.9561 (tp) cc_final: 0.9346 (tp) REVERT: C 976 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8180 (t70) REVERT: H 63 LYS cc_start: 0.3213 (pttt) cc_final: 0.2985 (mmmt) REVERT: D 48 MET cc_start: 0.1628 (mtm) cc_final: 0.1211 (ptm) REVERT: G 4 MET cc_start: 0.3856 (mmm) cc_final: 0.3358 (mtt) outliers start: 90 outliers final: 52 residues processed: 233 average time/residue: 0.3999 time to fit residues: 160.3164 Evaluate side-chains 179 residues out of total 3374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.636 > 50: distance: 8 - 10: 4.505 distance: 11 - 12: 4.346 distance: 12 - 13: 3.785 distance: 17 - 18: 5.532 distance: 17 - 138: 3.144 distance: 18 - 19: 9.783 distance: 18 - 21: 5.466 distance: 19 - 20: 14.160 distance: 19 - 25: 8.317 distance: 20 - 149: 17.149 distance: 21 - 22: 4.559 distance: 22 - 23: 3.885 distance: 25 - 26: 21.387 distance: 26 - 27: 12.420 distance: 26 - 29: 27.165 distance: 27 - 28: 18.118 distance: 27 - 31: 19.477 distance: 29 - 30: 23.506 distance: 31 - 32: 14.871 distance: 31 - 152: 7.272 distance: 32 - 33: 27.392 distance: 32 - 35: 21.425 distance: 33 - 34: 29.765 distance: 33 - 39: 27.549 distance: 35 - 36: 24.152 distance: 36 - 37: 14.414 distance: 36 - 38: 20.442 distance: 39 - 40: 5.678 distance: 40 - 41: 29.244 distance: 40 - 43: 34.459 distance: 41 - 42: 26.997 distance: 41 - 45: 25.170 distance: 43 - 44: 27.667 distance: 45 - 46: 13.312 distance: 45 - 51: 16.040 distance: 46 - 47: 9.882 distance: 46 - 49: 18.684 distance: 47 - 48: 13.600 distance: 47 - 52: 19.320 distance: 49 - 50: 23.087 distance: 50 - 51: 11.362 distance: 52 - 53: 12.870 distance: 53 - 54: 28.130 distance: 54 - 55: 16.490 distance: 54 - 56: 41.497 distance: 56 - 57: 9.319 distance: 57 - 58: 8.633 distance: 57 - 60: 26.408 distance: 58 - 59: 25.977 distance: 58 - 65: 18.865 distance: 60 - 61: 27.392 distance: 61 - 62: 3.226 distance: 62 - 64: 3.171 distance: 65 - 66: 8.496 distance: 66 - 67: 17.111 distance: 66 - 69: 18.743 distance: 67 - 68: 22.919 distance: 67 - 76: 19.139 distance: 69 - 70: 16.630 distance: 70 - 71: 7.775 distance: 76 - 77: 9.528 distance: 76 - 103: 8.465 distance: 77 - 78: 5.306 distance: 77 - 80: 11.084 distance: 78 - 79: 4.298 distance: 78 - 81: 6.953 distance: 79 - 100: 9.889