Starting phenix.real_space_refine (version: 1.21rc1) on Sun May 14 15:42:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/05_2023/7czs_30515.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/05_2023/7czs_30515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/05_2023/7czs_30515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/05_2023/7czs_30515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/05_2023/7czs_30515.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czs_30515/05_2023/7czs_30515.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 21759 2.51 5 N 5619 2.21 5 O 6802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 97": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ARG 97": "NH1" <-> "NH2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 97": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N GLU 165": "OE1" <-> "OE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 34321 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "K" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "M" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} 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: "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: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.15, per 1000 atoms: 0.50 Number of scatterers: 34321 At special positions: 0 Unit cell: (146.745, 175.007, 238.053, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 6802 8.00 N 5619 7.00 C 21759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.52 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.29 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.14 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 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=2.04 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 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.29 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.09 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.29 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.10 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 142 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 A1406 " - " NAG A1407 " " NAG B1409 " - " NAG B1410 " " NAG C1406 " - " NAG C1407 " " 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 L 1 " - " NAG L 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 331 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 343 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " Time building additional restraints: 13.93 Conformation dependent library (CDL) restraints added in 4.9 seconds 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8030 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 76 sheets defined 18.4% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) 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 754 removed outlier: 3.632A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.575A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.584A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) 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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.237A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.238A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 191 No H-bonds generated for 'chain 'I' and resid 189 through 191' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.237A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.571A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A 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 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.680A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) 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 539 through 543 removed outlier: 5.336A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.610A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.517A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.821A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.654A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.558A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.534A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 132 through 135 removed outlier: 4.139A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 193 through 194 removed outlier: 5.992A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 275 through 279 removed outlier: 3.888A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.118A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.863A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.605A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.530A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 152 through 156 Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.527A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG3, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG5, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'I' and resid 45 through 51 removed outlier: 6.530A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR I 33 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA I 139 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 186 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 141 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 184 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 143 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 182 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 145 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU I 180 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 123 through 126 removed outlier: 5.010A pdb=" N ALA I 139 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL I 186 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 141 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 184 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU I 143 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 182 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS I 145 " --> pdb=" O LEU I 180 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU I 180 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 152 through 156 Processing sheet with id=AH1, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AH3, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AH4, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AH6, first strand: chain 'J' and resid 45 through 51 removed outlier: 6.531A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AI1, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.526A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AI3, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AI4, first strand: chain 'N' and resid 153 through 154 1193 hydrogen bonds defined for protein. 3183 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: 14.99 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5730 1.32 - 1.45: 10423 1.45 - 1.58: 18739 1.58 - 1.72: 3 1.72 - 1.85: 174 Bond restraints: 35069 Sorted by residual: bond pdb=" CA HIS B 49 " pdb=" C HIS B 49 " ideal model delta sigma weight residual 1.520 1.405 0.115 1.22e-02 6.72e+03 8.96e+01 bond pdb=" CA GLN C 239 " pdb=" C GLN C 239 " ideal model delta sigma weight residual 1.525 1.420 0.105 1.11e-02 8.12e+03 8.92e+01 bond pdb=" CA ASN C 30 " pdb=" C ASN C 30 " ideal model delta sigma weight residual 1.520 1.415 0.105 1.16e-02 7.43e+03 8.16e+01 bond pdb=" CA ARG C 44 " pdb=" C ARG C 44 " ideal model delta sigma weight residual 1.521 1.414 0.107 1.24e-02 6.50e+03 7.38e+01 bond pdb=" CA TYR B 204 " pdb=" C TYR B 204 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.18e-02 7.18e+03 7.29e+01 ... (remaining 35064 not shown) Histogram of bond angle deviations from ideal: 96.92 - 105.24: 832 105.24 - 113.56: 19681 113.56 - 121.88: 19854 121.88 - 130.20: 7187 130.20 - 138.52: 146 Bond angle restraints: 47700 Sorted by residual: angle pdb=" CA PHE C 32 " pdb=" CB PHE C 32 " pdb=" CG PHE C 32 " ideal model delta sigma weight residual 113.80 103.50 10.30 1.00e+00 1.00e+00 1.06e+02 angle pdb=" CA GLN C 271 " pdb=" C GLN C 271 " pdb=" N PRO C 272 " ideal model delta sigma weight residual 117.82 125.26 -7.44 7.80e-01 1.64e+00 9.09e+01 angle pdb=" CA GLU C 224 " pdb=" C GLU C 224 " pdb=" O GLU C 224 " ideal model delta sigma weight residual 120.19 112.57 7.62 8.40e-01 1.42e+00 8.23e+01 angle pdb=" CA ASN B 188 " pdb=" CB ASN B 188 " pdb=" CG ASN B 188 " ideal model delta sigma weight residual 112.60 103.62 8.98 1.00e+00 1.00e+00 8.06e+01 angle pdb=" CA PHE C 238 " pdb=" CB PHE C 238 " pdb=" CG PHE C 238 " ideal model delta sigma weight residual 113.80 122.40 -8.60 1.00e+00 1.00e+00 7.40e+01 ... (remaining 47695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 17535 17.91 - 35.83: 2029 35.83 - 53.74: 568 53.74 - 71.66: 165 71.66 - 89.57: 65 Dihedral angle restraints: 20362 sinusoidal: 7863 harmonic: 12499 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.07 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.46 -63.46 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 156.45 -63.45 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 20359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5582 0.328 - 0.656: 33 0.656 - 0.984: 8 0.984 - 1.312: 2 1.312 - 1.640: 3 Chirality restraints: 5628 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.77 -1.63 2.00e-02 2.50e+03 6.62e+03 chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -3.45 1.05 2.00e-02 2.50e+03 2.73e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 5625 not shown) Planarity restraints: 6110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 282 " 0.243 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN B 282 " -0.115 2.00e-02 2.50e+03 pdb=" OD1 ASN B 282 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 282 " -0.561 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " 0.424 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 2 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG P 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG P 2 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG P 2 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG P 2 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.189 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" CG ASN C 657 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.388 2.00e-02 2.50e+03 pdb=" C1 NAG C1410 " -0.291 2.00e-02 2.50e+03 ... (remaining 6107 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 431 2.51 - 3.11: 25827 3.11 - 3.71: 49612 3.71 - 4.30: 74169 4.30 - 4.90: 122995 Nonbonded interactions: 273034 Sorted by model distance: nonbonded pdb=" O ARG C 273 " pdb=" OG1 THR C 274 " model vdw 1.914 2.440 nonbonded pdb=" O ALA C 522 " pdb=" OG1 THR C 523 " model vdw 1.923 2.440 nonbonded pdb=" O ASN A 334 " pdb=" ND2 ASN A 334 " model vdw 1.924 2.520 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.981 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 2.520 ... (remaining 273029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1410)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1410)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.340 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 86.290 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 : 0.013 0.117 35069 Z= 0.818 Angle : 1.301 13.517 47700 Z= 0.782 Chirality : 0.091 1.640 5628 Planarity : 0.010 0.302 6062 Dihedral : 17.817 89.571 12182 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 35.67 Ramachandran Plot: Outliers : 4.08 % Allowed : 11.55 % Favored : 84.38 % Rotamer Outliers : 12.67 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.11), residues: 4244 helix: -2.26 (0.16), residues: 683 sheet: -1.74 (0.14), residues: 1215 loop : -3.46 (0.11), residues: 2346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 474 poor density : 573 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 474 outliers final: 83 residues processed: 969 average time/residue: 0.4709 time to fit residues: 733.9388 Evaluate side-chains 365 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 282 time to evaluate : 3.781 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 2 residues processed: 83 average time/residue: 0.3730 time to fit residues: 61.0386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 0.4980 chunk 333 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 386 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 422 ASN A 440 ASN A 450 ASN A 498 GLN A 644 GLN A 658 ASN A 690 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 969 ASN A1101 HIS ** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 115 GLN B 188 ASN B 239 GLN B 245 HIS B 422 ASN B 440 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 498 GLN B 703 ASN B 901 GLN B 913 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 949 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 30 ASN C 87 ASN C 115 GLN C 388 ASN C 422 ASN C 440 ASN C 498 GLN C 542 ASN C 544 ASN C 641 ASN C 655 HIS C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS C1106 GLN H 166 HIS K 90 GLN M 37 GLN J 166 HIS N 37 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 35069 Z= 0.261 Angle : 0.847 13.787 47700 Z= 0.419 Chirality : 0.054 0.757 5628 Planarity : 0.006 0.059 6062 Dihedral : 5.623 28.371 4607 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.77 % Favored : 90.55 % Rotamer Outliers : 4.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.12), residues: 4244 helix: -0.20 (0.19), residues: 699 sheet: -0.82 (0.14), residues: 1201 loop : -2.92 (0.11), residues: 2344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 330 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 73 residues processed: 481 average time/residue: 0.4472 time to fit residues: 361.5340 Evaluate side-chains 307 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 234 time to evaluate : 3.815 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.3320 time to fit residues: 51.2712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 263 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 387 optimal weight: 30.0000 chunk 418 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 935 GLN B 87 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 804 GLN B 992 GLN C 207 HIS C 481 ASN C 536 ASN H 81 GLN M 6 GLN N 3 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 35069 Z= 0.303 Angle : 0.795 11.375 47700 Z= 0.391 Chirality : 0.052 0.521 5628 Planarity : 0.005 0.067 6062 Dihedral : 5.332 31.216 4607 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.66 % Favored : 89.92 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4244 helix: 0.46 (0.20), residues: 695 sheet: -0.44 (0.14), residues: 1197 loop : -2.65 (0.11), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 256 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 65 residues processed: 374 average time/residue: 0.4333 time to fit residues: 275.8041 Evaluate side-chains 276 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 211 time to evaluate : 3.608 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 65 outliers final: 1 residues processed: 65 average time/residue: 0.3163 time to fit residues: 44.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 42 optimal weight: 50.0000 chunk 184 optimal weight: 0.9980 chunk 260 optimal weight: 0.9990 chunk 388 optimal weight: 10.0000 chunk 411 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 368 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN B 30 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1058 HIS C 207 HIS H 39 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 35069 Z= 0.181 Angle : 0.691 15.107 47700 Z= 0.336 Chirality : 0.049 0.580 5628 Planarity : 0.005 0.060 6062 Dihedral : 4.896 27.163 4607 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.66 % Favored : 92.06 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4244 helix: 0.98 (0.20), residues: 688 sheet: -0.16 (0.15), residues: 1218 loop : -2.35 (0.12), residues: 2338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 246 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 33 residues processed: 337 average time/residue: 0.4255 time to fit residues: 248.2813 Evaluate side-chains 241 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 3.759 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.3212 time to fit residues: 25.3296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.0070 chunk 233 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 351 optimal weight: 5.9990 chunk 284 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 804 GLN C 207 HIS C 606 ASN C 804 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 35069 Z= 0.268 Angle : 0.734 11.498 47700 Z= 0.356 Chirality : 0.050 0.467 5628 Planarity : 0.005 0.060 6062 Dihedral : 4.980 27.869 4607 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.17 % Favored : 90.60 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4244 helix: 1.03 (0.20), residues: 690 sheet: -0.07 (0.15), residues: 1222 loop : -2.27 (0.12), residues: 2332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 229 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 53 residues processed: 322 average time/residue: 0.4309 time to fit residues: 236.3955 Evaluate side-chains 259 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 3.579 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.3293 time to fit residues: 37.6225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 1.9990 chunk 370 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 412 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 487 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 703 ASN B 804 GLN C 99 ASN H 166 HIS ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN M 6 GLN ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 35069 Z= 0.294 Angle : 0.734 13.907 47700 Z= 0.357 Chirality : 0.050 0.499 5628 Planarity : 0.005 0.060 6062 Dihedral : 5.057 32.217 4607 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.13 % Favored : 91.64 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4244 helix: 0.97 (0.20), residues: 690 sheet: -0.06 (0.15), residues: 1230 loop : -2.22 (0.12), residues: 2324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 215 time to evaluate : 4.093 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 42 residues processed: 285 average time/residue: 0.4278 time to fit residues: 209.7883 Evaluate side-chains 221 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 3.603 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.3183 time to fit residues: 30.2050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 230 optimal weight: 0.3980 chunk 410 optimal weight: 20.0000 chunk 256 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN B 81 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 160 GLN I 81 GLN M 89 GLN ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 35069 Z= 0.171 Angle : 0.664 12.154 47700 Z= 0.320 Chirality : 0.047 0.428 5628 Planarity : 0.004 0.067 6062 Dihedral : 4.735 29.753 4607 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.94 % Favored : 91.80 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4244 helix: 1.37 (0.20), residues: 692 sheet: 0.09 (0.15), residues: 1208 loop : -2.08 (0.12), residues: 2344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 3.759 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 243 average time/residue: 0.4592 time to fit residues: 192.1769 Evaluate side-chains 202 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 3.793 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3994 time to fit residues: 12.1567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 35069 Z= 0.267 Angle : 0.705 12.419 47700 Z= 0.341 Chirality : 0.049 0.435 5628 Planarity : 0.005 0.062 6062 Dihedral : 4.874 28.961 4607 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.81 % Favored : 90.93 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4244 helix: 1.28 (0.20), residues: 695 sheet: 0.09 (0.15), residues: 1192 loop : -2.11 (0.12), residues: 2357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 244 average time/residue: 0.4425 time to fit residues: 187.0538 Evaluate side-chains 210 residues out of total 3742 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3484 time to fit residues: 18.4948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9023 > 50: distance: 22 - 23: 12.452 distance: 23 - 24: 13.777 distance: 23 - 26: 14.390 distance: 24 - 25: 30.016 distance: 24 - 27: 20.948 distance: 27 - 28: 16.045 distance: 28 - 29: 15.284 distance: 28 - 31: 27.518 distance: 29 - 30: 38.051 distance: 29 - 35: 21.982 distance: 31 - 32: 13.204 distance: 32 - 33: 19.709 distance: 32 - 34: 23.821 distance: 35 - 36: 4.160 distance: 36 - 37: 14.056 distance: 36 - 39: 14.080 distance: 37 - 38: 37.896 distance: 37 - 42: 18.633 distance: 39 - 40: 22.092 distance: 39 - 41: 22.509 distance: 42 - 43: 11.768 distance: 43 - 44: 23.612 distance: 43 - 46: 18.353 distance: 44 - 45: 36.046 distance: 44 - 48: 11.386 distance: 46 - 47: 16.518 distance: 48 - 49: 14.769 distance: 49 - 50: 13.954 distance: 50 - 51: 18.714 distance: 50 - 52: 20.944 distance: 52 - 53: 11.816 distance: 53 - 54: 15.661 distance: 54 - 55: 22.336 distance: 54 - 59: 25.671 distance: 56 - 57: 20.275 distance: 56 - 58: 21.759 distance: 59 - 60: 12.256 distance: 59 - 121: 7.332 distance: 60 - 61: 10.264 distance: 60 - 63: 11.179 distance: 61 - 62: 17.371 distance: 61 - 69: 12.362 distance: 62 - 118: 16.159 distance: 63 - 64: 3.496 distance: 64 - 65: 15.761 distance: 64 - 66: 7.407 distance: 65 - 67: 6.537 distance: 66 - 68: 23.211 distance: 67 - 68: 5.844 distance: 69 - 70: 17.373 distance: 70 - 71: 25.066 distance: 70 - 73: 17.538 distance: 71 - 72: 43.330 distance: 71 - 76: 42.765 distance: 73 - 74: 14.192 distance: 73 - 75: 20.046 distance: 76 - 77: 31.796 distance: 77 - 78: 26.486 distance: 77 - 80: 24.232 distance: 78 - 79: 27.100 distance: 78 - 87: 16.623 distance: 80 - 81: 25.269 distance: 81 - 82: 26.170 distance: 81 - 83: 8.442 distance: 82 - 84: 12.078 distance: 83 - 85: 22.125 distance: 84 - 86: 12.462 distance: 85 - 86: 21.338 distance: 87 - 88: 4.671 distance: 87 - 93: 15.207 distance: 88 - 89: 21.787 distance: 88 - 91: 12.528 distance: 89 - 90: 18.704 distance: 89 - 94: 16.569 distance: 91 - 92: 9.107 distance: 92 - 93: 17.683