Starting phenix.real_space_refine on Mon Jul 6 23:21:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v82_31787/07_2026/7v82_31787.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.039 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 198 5.16 5 C 25566 2.51 5 N 6525 2.21 5 O 7803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40092 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "C" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.07, per 1000 atoms: 0.23 Number of scatterers: 40092 At special positions: 0 Unit cell: (167.2, 181.5, 242, 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 198 16.00 O 7803 8.00 N 6525 7.00 C 25566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.02 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 603 " " NAG A2006 " - " ASN A 657 " " NAG A2007 " - " ASN A 20 " " NAG A2008 " - " ASN A 188 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 165 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 343 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG B2007 " - " ASN B 20 " " NAG B2008 " - " ASN B 188 " " NAG C2001 " - " ASN C 61 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG C2008 " - " ASN C 20 " " NAG C2009 " - " ASN C 188 " " NAG D1001 " - " ASN D 53 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 343 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 282 " " NAG S 1 " - " ASN B 331 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 709 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 709 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9210 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 51 sheets defined 37.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.343A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.059A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.513A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.688A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.541A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.788A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.550A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.657A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.652A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.686A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.786A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.611A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.943A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.965A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.592A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.247A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.550A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.287A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.905A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.534A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.519A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.042A 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 826 removed outlier: 3.557A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.606A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.720A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.432A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.072A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.519A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 80 removed outlier: 4.230A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.627A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.910A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.647A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.671A pdb=" N TYR E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.921A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 224' Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.708A pdb=" N GLU E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.601A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.810A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 398 through 413 removed outlier: 4.268A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.688A pdb=" N ILE E 421 " --> pdb=" O HIS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.621A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 474 through 485 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.704A pdb=" N VAL E 506 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER E 507 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 507' Processing helix chain 'E' and resid 513 through 532 removed outlier: 4.180A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.661A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 3.640A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 582 through 588 removed outlier: 3.777A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 3.591A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.541A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.928A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.573A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'D' and resid 175 through 194 removed outlier: 3.960A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.677A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 4.035A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.581A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.091A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.750A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.751A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.603A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.525A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.884A pdb=" N SER D 507 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.695A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.679A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.564A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 582 through 588 removed outlier: 3.714A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.505A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 53 removed outlier: 4.293A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.808A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 128 removed outlier: 3.572A pdb=" N SER F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 removed outlier: 3.755A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 removed outlier: 3.715A pdb=" N ALA F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 194 removed outlier: 3.951A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.844A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.867A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.665A pdb=" N LYS F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 removed outlier: 3.867A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.290A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.633A pdb=" N VAL F 506 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.782A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.713A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.672A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 597 removed outlier: 3.556A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.732A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.454A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.954A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.027A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.984A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.019A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.452A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.723A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.840A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.054A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.799A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.360A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.558A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.670A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.567A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.915A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.119A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.042A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.770A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.052A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.684A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.991A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.633A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.950A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.138A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.005A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1670 hydrogen bonds defined for protein. 4686 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: 10.36 Time building geometry restraints manager: 4.88 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: 12688 1.34 - 1.46: 10170 1.46 - 1.58: 17920 1.58 - 1.70: 1 1.70 - 1.83: 288 Bond restraints: 41067 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" CB PRO E 492 " pdb=" CG PRO E 492 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" C1 NAG B2008 " pdb=" O5 NAG B2008 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 41062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 54575 1.85 - 3.71: 1130 3.71 - 5.56: 124 5.56 - 7.42: 23 7.42 - 9.27: 8 Bond angle restraints: 55860 Sorted by residual: angle pdb=" C LEU C 984 " pdb=" N ASP C 985 " pdb=" CA ASP C 985 " ideal model delta sigma weight residual 120.67 129.49 -8.82 1.34e+00 5.57e-01 4.34e+01 angle pdb=" CA PRO E 492 " pdb=" N PRO E 492 " pdb=" CD PRO E 492 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" C GLU E 375 " pdb=" N MET E 376 " pdb=" CA MET E 376 " ideal model delta sigma weight residual 121.58 114.21 7.37 1.95e+00 2.63e-01 1.43e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 114.04 109.55 4.49 1.24e+00 6.50e-01 1.31e+01 angle pdb=" N ILE F 21 " pdb=" CA ILE F 21 " pdb=" C ILE F 21 " ideal model delta sigma weight residual 113.42 109.28 4.14 1.17e+00 7.31e-01 1.25e+01 ... (remaining 55855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21322 17.93 - 35.86: 1932 35.86 - 53.79: 297 53.79 - 71.72: 81 71.72 - 89.65: 38 Dihedral angle restraints: 23670 sinusoidal: 9351 harmonic: 14319 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 -178.04 -88.96 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 177.81 -84.81 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 23667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 6077 0.096 - 0.192: 306 0.192 - 0.288: 5 0.288 - 0.385: 5 0.385 - 0.481: 1 Chirality restraints: 6394 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 6391 not shown) Planarity restraints: 7163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 491 " 0.091 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO E 492 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO E 492 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO E 492 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.030 2.00e-02 2.50e+03 2.79e-02 9.72e+00 pdb=" CG ASN C1074 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO C 987 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.039 5.00e-02 4.00e+02 ... (remaining 7160 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1169 2.70 - 3.25: 40074 3.25 - 3.80: 63496 3.80 - 4.35: 78915 4.35 - 4.90: 132798 Nonbonded interactions: 316452 Sorted by model distance: nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.150 3.040 nonbonded pdb=" O ASP B 442 " pdb=" ND2 ASN B 448 " model vdw 2.186 3.120 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.192 3.040 nonbonded pdb=" O ILE E 151 " pdb=" OG SER E 155 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP B 796 " pdb=" O6 NAG K 1 " model vdw 2.200 3.040 ... (remaining 316447 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' selection = chain 'B' selection = (chain 'C' and resid 14 through 2008) } ncs_group { reference = (chain 'D' and resid 19 through 614) selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } 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: 3.700 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: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 39.840 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.150 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:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.005 0.107 41197 Z= 0.209 Angle : 0.650 13.793 56202 Z= 0.326 Chirality : 0.046 0.481 6394 Planarity : 0.004 0.134 7110 Dihedral : 14.017 89.654 14316 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4848 helix: 1.24 (0.14), residues: 1592 sheet: 0.01 (0.18), residues: 747 loop : -1.40 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.021 0.001 TYR A 873 PHE 0.040 0.001 PHE C 906 TRP 0.035 0.001 TRP C 886 HIS 0.013 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (41067) covalent geometry : angle 0.62321 / 0.32 (55860) SS BOND : bond 0.00355 / 0.21 ( 48) SS BOND : angle 1.43973 / 1.01 ( 96) hydrogen bonds : bond 0.14104 / 9.17 ( 1670) hydrogen bonds : angle 5.94014 / 4.11 ( 4686) link_BETA1-4 : bond 0.00454 / 0.24 ( 29) link_BETA1-4 : angle 2.69391 / 2.16 ( 87) link_NAG-ASN : bond 0.00410 / 0.26 ( 53) link_NAG-ASN : angle 2.75207 / 1.73 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5302 (ppp) cc_final: 0.5060 (pp-130) REVERT: E 163 TRP cc_start: 0.8195 (m100) cc_final: 0.7553 (t60) REVERT: E 360 MET cc_start: 0.1436 (ptm) cc_final: -0.0109 (tpt) REVERT: E 480 MET cc_start: 0.1033 (mpp) cc_final: 0.0387 (ttp) REVERT: D 366 MET cc_start: 0.5490 (tpt) cc_final: 0.5127 (tpp) REVERT: F 332 MET cc_start: 0.1101 (ppp) cc_final: 0.0296 (pmm) REVERT: F 366 MET cc_start: 0.1461 (tpt) cc_final: 0.1176 (mmm) REVERT: F 462 MET cc_start: 0.6590 (ptm) cc_final: 0.6124 (mmt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.7953 time to fit residues: 116.8474 Evaluate side-chains 107 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 8.9990 chunk 470 optimal weight: 50.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 195 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.122147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.073724 restraints weight = 181368.922| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 6.74 r_work: 0.2840 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 41197 Z= 0.319 Angle : 0.683 11.003 56202 Z= 0.342 Chirality : 0.047 0.410 6394 Planarity : 0.004 0.073 7110 Dihedral : 4.396 26.455 5265 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.28 % Allowed : 6.35 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 4848 helix: 1.12 (0.13), residues: 1609 sheet: -0.01 (0.18), residues: 749 loop : -1.42 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.023 0.001 TYR F 385 PHE 0.032 0.002 PHE C 906 TRP 0.026 0.001 TRP C 886 HIS 0.014 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.32 (41067) covalent geometry : angle 0.66043 / 0.34 (55860) SS BOND : bond 0.00416 / 0.22 ( 48) SS BOND : angle 1.80193 / 1.29 ( 96) hydrogen bonds : bond 0.06075 / 3.97 ( 1670) hydrogen bonds : angle 5.22593 / 3.64 ( 4686) link_BETA1-4 : bond 0.00347 / 0.18 ( 29) link_BETA1-4 : angle 2.08609 / 1.62 ( 87) link_NAG-ASN : bond 0.00593 / 0.38 ( 53) link_NAG-ASN : angle 2.66192 / 1.69 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.6964 (ppp) cc_final: 0.6717 (pp-130) REVERT: C 153 MET cc_start: 0.7391 (tmm) cc_final: 0.7057 (tmm) REVERT: E 163 TRP cc_start: 0.8215 (m100) cc_final: 0.7972 (t60) REVERT: E 376 MET cc_start: 0.4675 (pmm) cc_final: 0.4178 (pmm) REVERT: D 332 MET cc_start: 0.6195 (pp-130) cc_final: 0.5885 (ppp) REVERT: F 366 MET cc_start: 0.3264 (tpt) cc_final: 0.3035 (mmm) outliers start: 12 outliers final: 2 residues processed: 111 average time/residue: 0.7830 time to fit residues: 106.1892 Evaluate side-chains 109 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain D residue 249 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 276 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 chunk 42 optimal weight: 50.0000 chunk 185 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.123651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.076832 restraints weight = 180930.297| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 6.27 r_work: 0.2906 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 41197 Z= 0.114 Angle : 0.555 10.114 56202 Z= 0.275 Chirality : 0.043 0.347 6394 Planarity : 0.004 0.071 7110 Dihedral : 4.063 22.912 5265 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.49 % Allowed : 8.89 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 4848 helix: 1.35 (0.13), residues: 1610 sheet: 0.15 (0.18), residues: 738 loop : -1.36 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 518 TYR 0.022 0.001 TYR F 385 PHE 0.014 0.001 PHE B1121 TRP 0.017 0.001 TRP E 610 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (41067) covalent geometry : angle 0.53641 / 0.27 (55860) SS BOND : bond 0.00318 / 0.18 ( 48) SS BOND : angle 1.23142 / 0.93 ( 96) hydrogen bonds : bond 0.04684 / 3.08 ( 1670) hydrogen bonds : angle 4.79206 / 3.32 ( 4686) link_BETA1-4 : bond 0.00478 / 0.26 ( 29) link_BETA1-4 : angle 2.03915 / 1.63 ( 87) link_NAG-ASN : bond 0.00403 / 0.26 ( 53) link_NAG-ASN : angle 2.18293 / 1.39 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.6202 (ppp) cc_final: 0.5819 (pp-130) REVERT: B 1132 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9128 (pp) REVERT: C 153 MET cc_start: 0.7364 (tmm) cc_final: 0.6744 (tmm) REVERT: E 163 TRP cc_start: 0.8181 (m100) cc_final: 0.7860 (t60) REVERT: E 480 MET cc_start: 0.2156 (ttt) cc_final: 0.1930 (tmm) REVERT: D 332 MET cc_start: 0.5380 (pp-130) cc_final: 0.4911 (ppp) REVERT: D 480 MET cc_start: 0.4826 (ppp) cc_final: 0.4507 (pp-130) REVERT: F 332 MET cc_start: 0.4097 (OUTLIER) cc_final: 0.3549 (tmm) REVERT: F 462 MET cc_start: 0.6331 (ptt) cc_final: 0.6043 (mmt) REVERT: F 480 MET cc_start: 0.5702 (pp-130) cc_final: 0.5316 (pp-130) outliers start: 21 outliers final: 6 residues processed: 116 average time/residue: 0.7852 time to fit residues: 111.1494 Evaluate side-chains 112 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 286 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 438 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 403 optimal weight: 20.0000 chunk 419 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 703 ASN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN E 239 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN F 81 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.122714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.082229 restraints weight = 180530.110| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 5.98 r_work: 0.2886 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 41197 Z= 0.209 Angle : 0.594 9.963 56202 Z= 0.295 Chirality : 0.044 0.391 6394 Planarity : 0.004 0.072 7110 Dihedral : 4.084 23.302 5265 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.12 % Allowed : 9.99 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 4848 helix: 1.37 (0.13), residues: 1607 sheet: 0.07 (0.18), residues: 733 loop : -1.31 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.019 0.001 TYR B1067 PHE 0.019 0.001 PHE A1121 TRP 0.016 0.001 TRP F 610 HIS 0.014 0.001 HIS E 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (41067) covalent geometry : angle 0.57506 / 0.29 (55860) SS BOND : bond 0.00362 / 0.19 ( 48) SS BOND : angle 1.41089 / 0.97 ( 96) hydrogen bonds : bond 0.05113 / 3.35 ( 1670) hydrogen bonds : angle 4.83245 / 3.36 ( 4686) link_BETA1-4 : bond 0.00350 / 0.18 ( 29) link_BETA1-4 : angle 2.03030 / 1.60 ( 87) link_NAG-ASN : bond 0.00430 / 0.28 ( 53) link_NAG-ASN : angle 2.29513 / 1.47 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.9466 (OUTLIER) cc_final: 0.8928 (ptm160) REVERT: B 108 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7694 (m) REVERT: B 153 MET cc_start: 0.5567 (ppp) cc_final: 0.5053 (pp-130) REVERT: B 984 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9181 (pp) REVERT: B 1132 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9219 (pp) REVERT: C 153 MET cc_start: 0.7045 (tmm) cc_final: 0.5896 (tmm) REVERT: C 1040 VAL cc_start: 0.9567 (OUTLIER) cc_final: 0.9365 (m) REVERT: E 163 TRP cc_start: 0.8150 (m100) cc_final: 0.7718 (t60) REVERT: E 480 MET cc_start: 0.2028 (ttt) cc_final: 0.1433 (tmm) REVERT: D 323 MET cc_start: 0.6864 (tmt) cc_final: 0.6564 (tmt) REVERT: D 332 MET cc_start: 0.4365 (pp-130) cc_final: 0.3818 (ppp) REVERT: D 474 MET cc_start: 0.3216 (tmt) cc_final: 0.3013 (tmt) REVERT: F 332 MET cc_start: 0.3722 (OUTLIER) cc_final: 0.2963 (tmm) REVERT: F 462 MET cc_start: 0.6312 (ptt) cc_final: 0.5772 (mmt) REVERT: F 480 MET cc_start: 0.5193 (pp-130) cc_final: 0.4639 (pp-130) outliers start: 48 outliers final: 15 residues processed: 138 average time/residue: 0.7340 time to fit residues: 125.7267 Evaluate side-chains 125 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 274 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 482 optimal weight: 30.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 241 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** 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 = 0.4478 r_free = 0.4478 target = 0.123608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.083316 restraints weight = 180866.690| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 6.69 r_work: 0.2882 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41197 Z= 0.109 Angle : 0.541 10.313 56202 Z= 0.267 Chirality : 0.043 0.353 6394 Planarity : 0.004 0.070 7110 Dihedral : 3.914 22.051 5265 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.00 % Allowed : 11.38 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 4848 helix: 1.49 (0.13), residues: 1609 sheet: 0.20 (0.19), residues: 731 loop : -1.26 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 460 TYR 0.020 0.001 TYR F 385 PHE 0.014 0.001 PHE E 592 TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (41067) covalent geometry : angle 0.52356 / 0.26 (55860) SS BOND : bond 0.00313 / 0.18 ( 48) SS BOND : angle 1.14451 / 0.80 ( 96) hydrogen bonds : bond 0.04354 / 2.87 ( 1670) hydrogen bonds : angle 4.62859 / 3.21 ( 4686) link_BETA1-4 : bond 0.00454 / 0.25 ( 29) link_BETA1-4 : angle 1.98677 / 1.58 ( 87) link_NAG-ASN : bond 0.00360 / 0.23 ( 53) link_NAG-ASN : angle 2.05165 / 1.31 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 670 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 1039 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8801 (ptm160) REVERT: B 108 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7652 (m) REVERT: B 153 MET cc_start: 0.5721 (ppp) cc_final: 0.5181 (pp-130) REVERT: B 581 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 984 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9119 (pp) REVERT: B 1132 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9233 (pp) REVERT: C 153 MET cc_start: 0.7004 (tmm) cc_final: 0.5773 (tmm) REVERT: E 163 TRP cc_start: 0.8153 (m100) cc_final: 0.7780 (t60) REVERT: E 480 MET cc_start: 0.2417 (ttt) cc_final: 0.1894 (tmm) REVERT: D 224 GLU cc_start: 0.8936 (mp0) cc_final: 0.8604 (pp20) REVERT: D 332 MET cc_start: 0.4861 (pp-130) cc_final: 0.4309 (ppp) REVERT: D 408 MET cc_start: 0.5816 (mmp) cc_final: 0.5282 (tpt) REVERT: D 455 MET cc_start: 0.4263 (OUTLIER) cc_final: 0.3998 (pp-130) REVERT: D 480 MET cc_start: 0.4518 (ppp) cc_final: 0.4120 (pp-130) REVERT: D 536 GLU cc_start: 0.8150 (pm20) cc_final: 0.7620 (tm-30) REVERT: F 332 MET cc_start: 0.3876 (OUTLIER) cc_final: 0.3112 (tmm) REVERT: F 462 MET cc_start: 0.6131 (ptt) cc_final: 0.5682 (mmt) REVERT: F 480 MET cc_start: 0.5507 (pp-130) cc_final: 0.5016 (pp-130) outliers start: 43 outliers final: 14 residues processed: 146 average time/residue: 0.7457 time to fit residues: 134.4275 Evaluate side-chains 129 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 323 optimal weight: 50.0000 chunk 481 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 407 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 393 optimal weight: 50.0000 chunk 31 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 389 optimal weight: 40.0000 chunk 377 optimal weight: 20.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN A 675 GLN A 955 ASN B 87 ASN C 360 ASN C 641 ASN E 90 ASN E 305 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN F 437 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.120093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.069814 restraints weight = 181172.831| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 6.71 r_work: 0.2757 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.241 41197 Z= 0.695 Angle : 0.967 14.146 56202 Z= 0.482 Chirality : 0.057 0.521 6394 Planarity : 0.005 0.077 7110 Dihedral : 4.786 25.965 5265 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.30 % Rotamer: Outliers : 1.79 % Allowed : 12.24 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4848 helix: 0.71 (0.13), residues: 1632 sheet: -0.40 (0.19), residues: 669 loop : -1.62 (0.11), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.033 0.002 TYR B 91 PHE 0.039 0.003 PHE A1121 TRP 0.028 0.002 TRP A 886 HIS 0.011 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01615 / 0.70 (41067) covalent geometry : angle 0.94438 / 0.48 (55860) SS BOND : bond 0.00607 / 0.32 ( 48) SS BOND : angle 2.57993 / 1.73 ( 96) hydrogen bonds : bond 0.07260 / 4.73 ( 1670) hydrogen bonds : angle 5.53709 / 3.86 ( 4686) link_BETA1-4 : bond 0.00817 / 0.51 ( 29) link_BETA1-4 : angle 2.46251 / 1.88 ( 87) link_NAG-ASN : bond 0.01195 / 0.78 ( 53) link_NAG-ASN : angle 3.14911 / 2.02 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 109 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.9325 (tt0) cc_final: 0.9025 (tm-30) REVERT: B 108 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7931 (m) REVERT: B 153 MET cc_start: 0.7011 (ppp) cc_final: 0.6608 (pp-130) REVERT: B 581 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9011 (p) REVERT: B 900 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9097 (ptm) REVERT: B 984 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9011 (pp) REVERT: C 153 MET cc_start: 0.7552 (tmm) cc_final: 0.6860 (tmm) REVERT: C 581 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8732 (p) REVERT: E 163 TRP cc_start: 0.8170 (m100) cc_final: 0.7959 (t60) REVERT: E 480 MET cc_start: 0.2685 (ttt) cc_final: 0.2125 (tmm) REVERT: D 332 MET cc_start: 0.6266 (pp-130) cc_final: 0.5916 (ppp) REVERT: D 408 MET cc_start: 0.5638 (mmp) cc_final: 0.5162 (tpt) REVERT: D 455 MET cc_start: 0.3517 (OUTLIER) cc_final: 0.3236 (pp-130) REVERT: D 480 MET cc_start: 0.4798 (ppp) cc_final: 0.4544 (pp-130) outliers start: 77 outliers final: 36 residues processed: 171 average time/residue: 0.6420 time to fit residues: 139.1424 Evaluate side-chains 147 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1057 PRO Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 260 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 198 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 465 optimal weight: 50.0000 chunk 344 optimal weight: 30.0000 chunk 449 optimal weight: 50.0000 chunk 145 optimal weight: 30.0000 chunk 430 optimal weight: 8.9990 chunk 156 optimal weight: 0.0980 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN E 397 ASN ** E 522 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 = 0.4454 r_free = 0.4454 target = 0.122444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.074228 restraints weight = 182342.646| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 6.62 r_work: 0.2836 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 41197 Z= 0.210 Angle : 0.637 11.897 56202 Z= 0.314 Chirality : 0.045 0.439 6394 Planarity : 0.004 0.075 7110 Dihedral : 4.378 24.112 5265 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.49 % Allowed : 13.04 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4848 helix: 1.08 (0.13), residues: 1634 sheet: -0.12 (0.18), residues: 720 loop : -1.47 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 518 TYR 0.021 0.001 TYR F 385 PHE 0.020 0.001 PHE A1121 TRP 0.013 0.001 TRP A 886 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (41067) covalent geometry : angle 0.61615 / 0.31 (55860) SS BOND : bond 0.00407 / 0.21 ( 48) SS BOND : angle 1.66571 / 1.14 ( 96) hydrogen bonds : bond 0.05399 / 3.53 ( 1670) hydrogen bonds : angle 4.99567 / 3.48 ( 4686) link_BETA1-4 : bond 0.00381 / 0.20 ( 29) link_BETA1-4 : angle 2.10976 / 1.69 ( 87) link_NAG-ASN : bond 0.00431 / 0.27 ( 53) link_NAG-ASN : angle 2.40115 / 1.52 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 106 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9036 (p) REVERT: A 1017 GLU cc_start: 0.9336 (tt0) cc_final: 0.9130 (tm-30) REVERT: A 1039 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.8973 (ptm160) REVERT: A 1132 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9123 (tt) REVERT: B 153 MET cc_start: 0.6664 (ppp) cc_final: 0.6197 (pp-130) REVERT: B 563 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: B 581 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9017 (p) REVERT: B 984 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9036 (pp) REVERT: C 153 MET cc_start: 0.7517 (tmm) cc_final: 0.6657 (tmm) REVERT: C 581 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8683 (p) REVERT: C 1040 VAL cc_start: 0.9555 (OUTLIER) cc_final: 0.9348 (m) REVERT: E 163 TRP cc_start: 0.8149 (m100) cc_final: 0.7871 (t60) REVERT: E 480 MET cc_start: 0.2387 (ttt) cc_final: 0.1802 (tmm) REVERT: E 610 TRP cc_start: 0.6517 (OUTLIER) cc_final: 0.6240 (p-90) REVERT: D 332 MET cc_start: 0.5738 (pp-130) cc_final: 0.5280 (ppp) REVERT: D 408 MET cc_start: 0.5980 (mmp) cc_final: 0.5427 (tpt) REVERT: D 455 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.3664 (pp-130) REVERT: D 480 MET cc_start: 0.4503 (ppp) cc_final: 0.4152 (pp-130) REVERT: F 123 MET cc_start: -0.0446 (OUTLIER) cc_final: -0.0827 (pmm) REVERT: F 332 MET cc_start: 0.4333 (OUTLIER) cc_final: 0.3845 (tmm) REVERT: F 480 MET cc_start: 0.6209 (pp-130) cc_final: 0.5965 (pp-130) outliers start: 64 outliers final: 17 residues processed: 156 average time/residue: 0.6783 time to fit residues: 132.8433 Evaluate side-chains 132 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 469 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 157 optimal weight: 0.3980 chunk 362 optimal weight: 40.0000 chunk 402 optimal weight: 0.0070 chunk 220 optimal weight: 9.9990 chunk 405 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 424 optimal weight: 2.9990 chunk 341 optimal weight: 40.0000 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** 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 = 0.4471 r_free = 0.4471 target = 0.123267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.080906 restraints weight = 180265.165| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 7.65 r_work: 0.2885 rms_B_bonded: 5.73 restraints_weight: 2.0000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41197 Z= 0.122 Angle : 0.582 11.515 56202 Z= 0.285 Chirality : 0.043 0.374 6394 Planarity : 0.004 0.071 7110 Dihedral : 4.063 23.264 5265 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.07 % Allowed : 13.90 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 4848 helix: 1.35 (0.13), residues: 1625 sheet: 0.03 (0.19), residues: 733 loop : -1.31 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 518 TYR 0.020 0.001 TYR F 385 PHE 0.015 0.001 PHE B1121 TRP 0.010 0.001 TRP C 104 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (41067) covalent geometry : angle 0.56490 / 0.28 (55860) SS BOND : bond 0.00368 / 0.21 ( 48) SS BOND : angle 1.26541 / 0.88 ( 96) hydrogen bonds : bond 0.04460 / 2.94 ( 1670) hydrogen bonds : angle 4.72487 / 3.28 ( 4686) link_BETA1-4 : bond 0.00469 / 0.25 ( 29) link_BETA1-4 : angle 2.02568 / 1.62 ( 87) link_NAG-ASN : bond 0.00345 / 0.22 ( 53) link_NAG-ASN : angle 2.08998 / 1.33 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9046 (p) REVERT: A 1039 ARG cc_start: 0.9408 (OUTLIER) cc_final: 0.8876 (ptm160) REVERT: B 153 MET cc_start: 0.6021 (ppp) cc_final: 0.5395 (pp-130) REVERT: B 581 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8917 (p) REVERT: B 984 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9081 (pp) REVERT: C 153 MET cc_start: 0.7047 (tmm) cc_final: 0.5822 (tmm) REVERT: C 581 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8741 (p) REVERT: E 163 TRP cc_start: 0.8149 (m100) cc_final: 0.7716 (t60) REVERT: E 480 MET cc_start: 0.1936 (ttt) cc_final: 0.1335 (tmm) REVERT: E 610 TRP cc_start: 0.5775 (OUTLIER) cc_final: 0.5308 (p-90) REVERT: D 224 GLU cc_start: 0.8939 (mp0) cc_final: 0.8583 (pp20) REVERT: D 332 MET cc_start: 0.4697 (pp-130) cc_final: 0.4269 (pp-130) REVERT: D 408 MET cc_start: 0.6248 (mmp) cc_final: 0.5625 (tpt) REVERT: D 536 GLU cc_start: 0.8116 (mp0) cc_final: 0.7694 (tm-30) REVERT: F 332 MET cc_start: 0.3596 (OUTLIER) cc_final: 0.1691 (ppp) REVERT: F 383 MET cc_start: 0.7374 (pp-130) cc_final: 0.6016 (pmm) REVERT: F 462 MET cc_start: 0.5259 (ptt) cc_final: 0.4816 (mmt) REVERT: F 480 MET cc_start: 0.5516 (pp-130) cc_final: 0.4786 (pp-130) outliers start: 46 outliers final: 17 residues processed: 144 average time/residue: 0.6933 time to fit residues: 123.7567 Evaluate side-chains 131 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.1656 > 50: distance: 66 - 70: 11.269 distance: 70 - 71: 17.846 distance: 70 - 76: 24.609 distance: 71 - 74: 25.475 distance: 72 - 73: 22.383 distance: 72 - 77: 10.770 distance: 74 - 75: 22.857 distance: 75 - 76: 4.074 distance: 77 - 78: 14.413 distance: 78 - 79: 28.035 distance: 78 - 81: 29.177 distance: 79 - 80: 24.268 distance: 79 - 85: 10.347 distance: 81 - 82: 23.204 distance: 81 - 83: 16.688 distance: 82 - 84: 19.580 distance: 85 - 86: 5.929 distance: 86 - 87: 28.705 distance: 87 - 88: 16.005 distance: 87 - 89: 24.582 distance: 89 - 90: 21.588 distance: 90 - 91: 23.535 distance: 90 - 93: 23.647 distance: 91 - 92: 18.592 distance: 91 - 95: 28.050 distance: 93 - 94: 27.929 distance: 95 - 96: 17.078 distance: 96 - 97: 13.459 distance: 96 - 99: 27.727 distance: 97 - 98: 26.055 distance: 97 - 103: 19.105 distance: 99 - 100: 21.304 distance: 100 - 101: 18.918 distance: 100 - 102: 56.811 distance: 103 - 104: 31.295 distance: 103 - 109: 13.781 distance: 104 - 105: 26.000 distance: 104 - 107: 14.767 distance: 105 - 106: 16.906 distance: 105 - 110: 27.125 distance: 107 - 108: 31.686 distance: 108 - 109: 10.955 distance: 110 - 111: 4.380 distance: 111 - 112: 18.645 distance: 111 - 114: 7.106 distance: 112 - 113: 9.524 distance: 112 - 115: 5.121 distance: 115 - 116: 10.213 distance: 116 - 117: 7.103 distance: 116 - 119: 7.712 distance: 117 - 118: 15.433 distance: 117 - 125: 6.822 distance: 119 - 120: 15.929 distance: 120 - 121: 15.887 distance: 120 - 122: 20.503 distance: 121 - 123: 10.246 distance: 122 - 124: 5.902 distance: 123 - 124: 18.753 distance: 125 - 126: 9.595 distance: 126 - 127: 9.910 distance: 126 - 129: 15.896 distance: 127 - 128: 23.316 distance: 127 - 133: 19.575 distance: 129 - 130: 21.348 distance: 130 - 131: 19.093 distance: 130 - 132: 28.306 distance: 133 - 134: 26.169 distance: 134 - 135: 30.475 distance: 134 - 137: 38.136 distance: 135 - 136: 31.652 distance: 135 - 141: 20.695 distance: 137 - 138: 32.379 distance: 138 - 139: 3.084 distance: 138 - 140: 26.302