Starting phenix.real_space_refine on Mon Apr 15 08:23:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvo_12608/04_2024/7nvo_12608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvo_12608/04_2024/7nvo_12608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvo_12608/04_2024/7nvo_12608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvo_12608/04_2024/7nvo_12608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvo_12608/04_2024/7nvo_12608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvo_12608/04_2024/7nvo_12608_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Al 12 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 188 5.16 5 C 21290 2.51 5 N 5946 2.21 5 O 6726 1.98 5 F 36 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 27": "NH1" <-> "NH2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "E ARG 534": "NH1" <-> "NH2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H ARG 421": "NH1" <-> "NH2" Residue "H GLU 482": "OE1" <-> "OE2" Residue "H GLU 494": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 94": "OE1" <-> "OE2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q GLU 117": "OE1" <-> "OE2" Residue "Q GLU 130": "OE1" <-> "OE2" Residue "Q GLU 141": "OE1" <-> "OE2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q GLU 389": "OE1" <-> "OE2" Residue "Q GLU 434": "OE1" <-> "OE2" Residue "Q GLU 483": "OE1" <-> "OE2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z GLU 142": "OE1" <-> "OE2" Residue "Z GLU 415": "OE1" <-> "OE2" Residue "Z GLU 420": "OE1" <-> "OE2" Residue "Z GLU 469": "OE1" <-> "OE2" Residue "Z GLU 485": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 433": "OE1" <-> "OE2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "G GLU 492": "OE1" <-> "OE2" Residue "G GLU 511": "OE1" <-> "OE2" Residue "G ARG 518": "NH1" <-> "NH2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 99": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "e ARG 27": "NH1" <-> "NH2" Residue "e GLU 101": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "e GLU 138": "OE1" <-> "OE2" Residue "e GLU 426": "OE1" <-> "OE2" Residue "e GLU 444": "OE1" <-> "OE2" Residue "e GLU 456": "OE1" <-> "OE2" Residue "e GLU 464": "OE1" <-> "OE2" Residue "e GLU 508": "OE1" <-> "OE2" Residue "e ARG 534": "NH1" <-> "NH2" Residue "h GLU 34": "OE1" <-> "OE2" Residue "h GLU 113": "OE1" <-> "OE2" Residue "h ARG 421": "NH1" <-> "NH2" Residue "h GLU 482": "OE1" <-> "OE2" Residue "h GLU 494": "OE1" <-> "OE2" Residue "q GLU 61": "OE1" <-> "OE2" Residue "q GLU 94": "OE1" <-> "OE2" Residue "q GLU 96": "OE1" <-> "OE2" Residue "q GLU 113": "OE1" <-> "OE2" Residue "q GLU 117": "OE1" <-> "OE2" Residue "q GLU 130": "OE1" <-> "OE2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "q GLU 176": "OE1" <-> "OE2" Residue "q GLU 389": "OE1" <-> "OE2" Residue "q GLU 434": "OE1" <-> "OE2" Residue "q GLU 483": "OE1" <-> "OE2" Residue "z GLU 12": "OE1" <-> "OE2" Residue "z GLU 66": "OE1" <-> "OE2" Residue "z GLU 142": "OE1" <-> "OE2" Residue "z GLU 415": "OE1" <-> "OE2" Residue "z GLU 420": "OE1" <-> "OE2" Residue "z GLU 469": "OE1" <-> "OE2" Residue "z GLU 485": "OE1" <-> "OE2" Residue "g ARG 38": "NH1" <-> "NH2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 433": "OE1" <-> "OE2" Residue "g ARG 467": "NH1" <-> "NH2" Residue "g GLU 492": "OE1" <-> "OE2" Residue "g GLU 511": "OE1" <-> "OE2" Residue "g ARG 518": "NH1" <-> "NH2" Residue "a GLU 85": "OE1" <-> "OE2" Residue "a GLU 99": "OE1" <-> "OE2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a GLU 473": "OE1" <-> "OE2" Residue "a GLU 505": "OE1" <-> "OE2" Residue "a GLU 519": "OE1" <-> "OE2" Residue "d ARG 34": "NH1" <-> "NH2" Residue "d ASP 63": "OD1" <-> "OD2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 135": "OE1" <-> "OE2" Residue "d GLU 142": "OE1" <-> "OE2" Residue "d GLU 479": "OE1" <-> "OE2" Residue "d GLU 506": "OE1" <-> "OE2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b GLU 112": "OE1" <-> "OE2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b GLU 152": "OE1" <-> "OE2" Residue "b GLU 385": "OE1" <-> "OE2" Residue "b GLU 387": "OE1" <-> "OE2" Residue "b GLU 414": "OE1" <-> "OE2" Residue "b ASP 460": "OD1" <-> "OD2" Residue "b GLU 482": "OE1" <-> "OE2" Residue "b GLU 495": "OE1" <-> "OE2" Residue "b GLU 509": "OE1" <-> "OE2" Residue "n GLU 6": "OE1" <-> "OE2" Residue "n ARG 99": "NH1" <-> "NH2" Residue "n ARG 103": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34246 Number of models: 1 Model: "" Number of chains: 42 Chain: "E" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1873 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "H" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1900 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 1 Chain: "Q" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2685 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 1 Chain: "Z" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2417 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 8, 'TRANS': 314} Chain breaks: 1 Chain: "G" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1880 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1879 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 1840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 bond proxies already assigned to first conformer: 1831 Chain: "B" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2073 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 323 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 2 Chain: "e" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1873 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "h" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1900 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 1 Chain: "q" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2685 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 9, 'TRANS': 342} Chain breaks: 1 Chain: "z" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2417 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 8, 'TRANS': 314} Chain breaks: 1 Chain: "g" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1880 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1879 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 8, 'TRANS': 240} Chain breaks: 1 Chain: "d" Number of atoms: 1840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 247, 1829 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 1 bond proxies already assigned to first conformer: 1831 Chain: "b" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2073 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 323 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE D 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 35 " occ=0.50 residue: pdb=" N APHE d 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE d 35 " occ=0.50 Time building chain proxies: 19.11, per 1000 atoms: 0.56 Number of scatterers: 34246 At special positions: 0 Unit cell: (181.26, 114.48, 174.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 188 16.00 P 32 15.00 Al 12 13.00 Mg 16 11.99 F 36 9.00 O 6726 8.00 N 5946 7.00 C 21290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM34226 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM33978 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM33790 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM34038 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM34102 O3A ADP z 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM33854 O3A ADP Z 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM34070 O3A ADP q 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM33918 O3A ADP A 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM34166 O3A ADP a 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.17 Conformation dependent library (CDL) restraints added in 6.6 seconds 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 32 sheets defined 53.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.50 Creating SS restraints... Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.622A pdb=" N MET E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 removed outlier: 4.458A pdb=" N SER E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 97 removed outlier: 3.811A pdb=" N LYS E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.885A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 removed outlier: 3.505A pdb=" N ASP E 149 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 439 removed outlier: 3.548A pdb=" N ALA E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 461 removed outlier: 3.952A pdb=" N GLU E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE E 458 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 481 removed outlier: 4.146A pdb=" N ARG E 480 " --> pdb=" O GLU E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 516 through 527 removed outlier: 3.797A pdb=" N THR E 521 " --> pdb=" O ILE E 517 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 34 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 63 through 68 removed outlier: 4.146A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 89 Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 118 through 125 Processing helix chain 'H' and resid 127 through 139 Processing helix chain 'H' and resid 416 through 426 removed outlier: 4.290A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.635A pdb=" N LEU H 433 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU H 434 " --> pdb=" O GLN H 431 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE H 435 " --> pdb=" O GLN H 432 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY H 436 " --> pdb=" O LEU H 433 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA H 439 " --> pdb=" O GLY H 436 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS H 440 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 453 removed outlier: 4.334A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA H 453 " --> pdb=" O LEU H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 470 removed outlier: 4.092A pdb=" N ASN H 462 " --> pdb=" O THR H 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN H 470 " --> pdb=" O ALA H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 514 Processing helix chain 'Q' and resid 29 through 46 removed outlier: 3.590A pdb=" N ILE Q 33 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 76 Processing helix chain 'Q' and resid 81 through 96 removed outlier: 3.937A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 119 removed outlier: 3.880A pdb=" N ALA Q 108 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY Q 109 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA Q 110 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 145 removed outlier: 3.735A pdb=" N GLU Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY Q 131 " --> pdb=" O GLU Q 127 " (cutoff:3.500A) Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 161 Processing helix chain 'Q' and resid 165 through 169 Processing helix chain 'Q' and resid 176 through 189 removed outlier: 3.639A pdb=" N ALA Q 186 " --> pdb=" O LEU Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 386 through 404 Processing helix chain 'Q' and resid 414 through 429 Processing helix chain 'Q' and resid 433 through 454 removed outlier: 3.532A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU Q 446 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) Proline residue: Q 449 - end of helix removed outlier: 3.990A pdb=" N GLU Q 454 " --> pdb=" O ALA Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 473 removed outlier: 3.652A pdb=" N VAL Q 470 " --> pdb=" O LYS Q 466 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU Q 473 " --> pdb=" O ALA Q 469 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 520 removed outlier: 3.670A pdb=" N ALA Q 507 " --> pdb=" O GLY Q 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 37 removed outlier: 3.632A pdb=" N VAL Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 64 No H-bonds generated for 'chain 'Z' and resid 61 through 64' Processing helix chain 'Z' and resid 72 through 84 removed outlier: 3.588A pdb=" N ALA Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN Z 84 " --> pdb=" O VAL Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 102 Processing helix chain 'Z' and resid 105 through 111 removed outlier: 4.410A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 135 removed outlier: 4.189A pdb=" N GLU Z 121 " --> pdb=" O ARG Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 156 removed outlier: 3.898A pdb=" N SER Z 155 " --> pdb=" O VAL Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 173 Processing helix chain 'Z' and resid 384 through 404 removed outlier: 3.656A pdb=" N ASP Z 404 " --> pdb=" O ASN Z 400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 428 removed outlier: 3.535A pdb=" N LEU Z 422 " --> pdb=" O MET Z 418 " (cutoff:3.500A) Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 432 through 437 Processing helix chain 'Z' and resid 446 through 455 removed outlier: 3.616A pdb=" N SER Z 455 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 461 through 473 Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 501 through 516 removed outlier: 3.760A pdb=" N LEU Z 505 " --> pdb=" O LYS Z 501 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS Z 506 " --> pdb=" O LYS Z 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.613A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 96 through 99 No H-bonds generated for 'chain 'G' and resid 96 through 99' Processing helix chain 'G' and resid 104 through 107 No H-bonds generated for 'chain 'G' and resid 104 through 107' Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.511A pdb=" N LEU G 113 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 136 removed outlier: 3.804A pdb=" N LYS G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER G 135 " --> pdb=" O ASP G 131 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 428 removed outlier: 4.036A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 443 Processing helix chain 'G' and resid 446 through 453 Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.909A pdb=" N SER G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 503 through 515 removed outlier: 3.585A pdb=" N VAL G 514 " --> pdb=" O VAL G 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.904A pdb=" N LYS A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.937A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 414 through 428 removed outlier: 3.864A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 448 through 451 No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 481 through 484 removed outlier: 3.783A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 481 through 484' Processing helix chain 'A' and resid 507 through 525 removed outlier: 3.584A pdb=" N LYS A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 33 No H-bonds generated for 'chain 'D' and resid 30 through 33' Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.514A pdb=" N LEU D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 125 removed outlier: 4.099A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 147 removed outlier: 3.996A pdb=" N LYS D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 439 removed outlier: 3.973A pdb=" N LEU D 432 " --> pdb=" O PRO D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 458 removed outlier: 5.793A pdb=" N VAL D 451 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D 452 " --> pdb=" O TYR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 468 Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.991A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.621A pdb=" N ALA B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 141 removed outlier: 3.619A pdb=" N ILE B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.600A pdb=" N ARG B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 402 Processing helix chain 'B' and resid 412 through 425 Processing helix chain 'B' and resid 433 through 452 removed outlier: 3.502A pdb=" N SER B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 458 through 470 removed outlier: 4.155A pdb=" N ALA B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'e' and resid 36 through 41 Processing helix chain 'e' and resid 43 through 50 removed outlier: 3.622A pdb=" N MET e 48 " --> pdb=" O VAL e 44 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 removed outlier: 4.458A pdb=" N SER e 79 " --> pdb=" O ALA e 75 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N MET e 80 " --> pdb=" O THR e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 97 removed outlier: 3.813A pdb=" N LYS e 96 " --> pdb=" O VAL e 92 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER e 97 " --> pdb=" O GLU e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 126 removed outlier: 3.885A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP e 125 " --> pdb=" O GLU e 121 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG e 126 " --> pdb=" O GLN e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 removed outlier: 3.506A pdb=" N ASP e 149 " --> pdb=" O ILE e 145 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS e 150 " --> pdb=" O GLU e 146 " (cutoff:3.500A) Processing helix chain 'e' and resid 425 through 439 removed outlier: 3.547A pdb=" N ALA e 430 " --> pdb=" O GLU e 426 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN e 435 " --> pdb=" O LEU e 431 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP e 438 " --> pdb=" O SER e 434 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 443 through 461 removed outlier: 3.950A pdb=" N GLU e 456 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE e 458 " --> pdb=" O LEU e 455 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 481 removed outlier: 4.145A pdb=" N ARG e 480 " --> pdb=" O GLU e 476 " (cutoff:3.500A) Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 516 through 527 removed outlier: 3.798A pdb=" N THR e 521 " --> pdb=" O ILE e 517 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET e 526 " --> pdb=" O GLN e 522 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 34 Processing helix chain 'h' and resid 37 through 39 No H-bonds generated for 'chain 'h' and resid 37 through 39' Processing helix chain 'h' and resid 63 through 68 removed outlier: 4.145A pdb=" N LEU h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 74 through 89 Processing helix chain 'h' and resid 96 through 106 Processing helix chain 'h' and resid 109 through 112 No H-bonds generated for 'chain 'h' and resid 109 through 112' Processing helix chain 'h' and resid 118 through 125 Processing helix chain 'h' and resid 127 through 139 Processing helix chain 'h' and resid 416 through 426 removed outlier: 4.290A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 442 removed outlier: 3.636A pdb=" N LEU h 433 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU h 434 " --> pdb=" O GLN h 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE h 435 " --> pdb=" O GLN h 432 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY h 436 " --> pdb=" O LEU h 433 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA h 439 " --> pdb=" O GLY h 436 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS h 440 " --> pdb=" O ALA h 437 " (cutoff:3.500A) Processing helix chain 'h' and resid 445 through 453 removed outlier: 4.333A pdb=" N CYS h 450 " --> pdb=" O PRO h 446 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA h 453 " --> pdb=" O LEU h 449 " (cutoff:3.500A) Processing helix chain 'h' and resid 457 through 470 removed outlier: 4.093A pdb=" N ASN h 462 " --> pdb=" O THR h 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN h 470 " --> pdb=" O ALA h 466 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 514 Processing helix chain 'q' and resid 29 through 46 removed outlier: 3.590A pdb=" N ILE q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU q 38 " --> pdb=" O GLN q 34 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 76 Processing helix chain 'q' and resid 81 through 96 removed outlier: 3.937A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 103 through 119 removed outlier: 3.880A pdb=" N ALA q 108 " --> pdb=" O VAL q 104 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY q 109 " --> pdb=" O LEU q 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA q 110 " --> pdb=" O VAL q 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 145 removed outlier: 3.736A pdb=" N GLU q 130 " --> pdb=" O SER q 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY q 131 " --> pdb=" O GLU q 127 " (cutoff:3.500A) Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 161 Processing helix chain 'q' and resid 165 through 169 Processing helix chain 'q' and resid 176 through 189 removed outlier: 3.640A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 386 through 404 Processing helix chain 'q' and resid 414 through 429 Processing helix chain 'q' and resid 433 through 454 removed outlier: 3.533A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU q 446 " --> pdb=" O GLU q 443 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 3.991A pdb=" N GLU q 454 " --> pdb=" O ALA q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 473 removed outlier: 3.651A pdb=" N VAL q 470 " --> pdb=" O LYS q 466 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 501 through 520 removed outlier: 3.669A pdb=" N ALA q 507 " --> pdb=" O GLY q 503 " (cutoff:3.500A) Processing helix chain 'z' and resid 17 through 37 removed outlier: 3.632A pdb=" N VAL z 22 " --> pdb=" O ALA z 18 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 61 through 64 No H-bonds generated for 'chain 'z' and resid 61 through 64' Processing helix chain 'z' and resid 72 through 84 removed outlier: 3.588A pdb=" N ALA z 83 " --> pdb=" O LYS z 79 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN z 84 " --> pdb=" O VAL z 80 " (cutoff:3.500A) Processing helix chain 'z' and resid 95 through 102 Processing helix chain 'z' and resid 105 through 111 removed outlier: 4.410A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 135 removed outlier: 4.189A pdb=" N GLU z 121 " --> pdb=" O ARG z 117 " (cutoff:3.500A) Processing helix chain 'z' and resid 145 through 156 removed outlier: 3.897A pdb=" N SER z 155 " --> pdb=" O VAL z 151 " (cutoff:3.500A) Processing helix chain 'z' and resid 168 through 173 Processing helix chain 'z' and resid 384 through 404 removed outlier: 3.657A pdb=" N ASP z 404 " --> pdb=" O ASN z 400 " (cutoff:3.500A) Processing helix chain 'z' and resid 413 through 428 removed outlier: 3.535A pdb=" N LEU z 422 " --> pdb=" O MET z 418 " (cutoff:3.500A) Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 437 Processing helix chain 'z' and resid 446 through 455 removed outlier: 3.615A pdb=" N SER z 455 " --> pdb=" O LEU z 451 " (cutoff:3.500A) Processing helix chain 'z' and resid 461 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 501 through 516 removed outlier: 3.759A pdb=" N LEU z 505 " --> pdb=" O LYS z 501 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS z 506 " --> pdb=" O LYS z 502 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 37 removed outlier: 3.613A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 Processing helix chain 'g' and resid 75 through 88 Processing helix chain 'g' and resid 96 through 99 No H-bonds generated for 'chain 'g' and resid 96 through 99' Processing helix chain 'g' and resid 104 through 107 No H-bonds generated for 'chain 'g' and resid 104 through 107' Processing helix chain 'g' and resid 109 through 113 removed outlier: 3.511A pdb=" N LEU g 113 " --> pdb=" O GLU g 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 136 removed outlier: 3.804A pdb=" N LYS g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP g 132 " --> pdb=" O LYS g 128 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER g 135 " --> pdb=" O ASP g 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR g 136 " --> pdb=" O ASP g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 413 through 428 removed outlier: 4.035A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 435 through 443 Processing helix chain 'g' and resid 446 through 453 Processing helix chain 'g' and resid 459 through 471 removed outlier: 3.909A pdb=" N SER g 465 " --> pdb=" O ARG g 461 " (cutoff:3.500A) Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 503 through 515 removed outlier: 3.584A pdb=" N VAL g 514 " --> pdb=" O VAL g 510 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 32 Processing helix chain 'a' and resid 58 through 64 removed outlier: 3.905A pdb=" N LYS a 63 " --> pdb=" O ALA a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 110 removed outlier: 3.938A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE a 95 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 128 Processing helix chain 'a' and resid 132 through 134 No H-bonds generated for 'chain 'a' and resid 132 through 134' Processing helix chain 'a' and resid 414 through 428 removed outlier: 3.865A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 439 through 442 No H-bonds generated for 'chain 'a' and resid 439 through 442' Processing helix chain 'a' and resid 448 through 451 No H-bonds generated for 'chain 'a' and resid 448 through 451' Processing helix chain 'a' and resid 461 through 470 Processing helix chain 'a' and resid 472 through 474 No H-bonds generated for 'chain 'a' and resid 472 through 474' Processing helix chain 'a' and resid 481 through 484 removed outlier: 3.783A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 481 through 484' Processing helix chain 'a' and resid 507 through 525 removed outlier: 3.584A pdb=" N LYS a 512 " --> pdb=" O ILE a 508 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU a 519 " --> pdb=" O LYS a 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 33 No H-bonds generated for 'chain 'd' and resid 30 through 33' Processing helix chain 'd' and resid 49 through 51 No H-bonds generated for 'chain 'd' and resid 49 through 51' Processing helix chain 'd' and resid 74 through 79 Processing helix chain 'd' and resid 86 through 101 removed outlier: 3.514A pdb=" N LEU d 94 " --> pdb=" O MET d 90 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER d 95 " --> pdb=" O LEU d 91 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS d 96 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 125 removed outlier: 4.099A pdb=" N LEU d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 147 removed outlier: 3.995A pdb=" N LYS d 143 " --> pdb=" O LYS d 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 427 through 439 removed outlier: 3.973A pdb=" N LEU d 432 " --> pdb=" O PRO d 428 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 458 removed outlier: 5.793A pdb=" N VAL d 451 " --> pdb=" O SER d 448 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG d 452 " --> pdb=" O TYR d 449 " (cutoff:3.500A) Processing helix chain 'd' and resid 461 through 468 Processing helix chain 'd' and resid 473 through 485 Processing helix chain 'd' and resid 512 through 530 Processing helix chain 'b' and resid 30 through 38 Processing helix chain 'b' and resid 79 through 93 removed outlier: 3.991A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET b 87 " --> pdb=" O VAL b 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG b 89 " --> pdb=" O VAL b 85 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL b 90 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 118 removed outlier: 3.621A pdb=" N ALA b 106 " --> pdb=" O VAL b 102 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU b 112 " --> pdb=" O GLU b 108 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 141 removed outlier: 3.619A pdb=" N ILE b 127 " --> pdb=" O PRO b 123 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA b 128 " --> pdb=" O GLN b 124 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU b 132 " --> pdb=" O ALA b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 164 removed outlier: 3.600A pdb=" N ARG b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN b 157 " --> pdb=" O VAL b 153 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET b 160 " --> pdb=" O ARG b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 386 through 402 Processing helix chain 'b' and resid 412 through 425 Processing helix chain 'b' and resid 433 through 452 removed outlier: 3.502A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET b 445 " --> pdb=" O LYS b 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU b 446 " --> pdb=" O ALA b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 458 through 470 removed outlier: 4.154A pdb=" N ALA b 463 " --> pdb=" O ALA b 459 " (cutoff:3.500A) Processing helix chain 'b' and resid 497 through 515 Processing sheet with id= A, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= B, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= C, first strand: chain 'H' and resid 48 through 50 Processing sheet with id= D, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= E, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= F, first strand: chain 'Q' and resid 54 through 56 removed outlier: 4.156A pdb=" N VAL Q 56 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE Q 64 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= I, first strand: chain 'G' and resid 48 through 50 Processing sheet with id= J, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= K, first strand: chain 'G' and resid 478 through 481 removed outlier: 4.009A pdb=" N THR G 486 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 43 through 45 removed outlier: 3.705A pdb=" N THR A 53 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.853A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= O, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= P, first strand: chain 'N' and resid 33 through 35 removed outlier: 3.832A pdb=" N ASP N 33 " --> pdb=" O ASN N 98 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'e' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= S, first strand: chain 'h' and resid 48 through 50 Processing sheet with id= T, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= U, first strand: chain 'h' and resid 475 through 477 Processing sheet with id= V, first strand: chain 'q' and resid 54 through 56 removed outlier: 4.156A pdb=" N VAL q 56 " --> pdb=" O PHE q 64 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE q 64 " --> pdb=" O VAL q 56 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= X, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= Y, first strand: chain 'g' and resid 48 through 50 Processing sheet with id= Z, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= AA, first strand: chain 'g' and resid 478 through 481 removed outlier: 4.009A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'a' and resid 43 through 45 removed outlier: 3.705A pdb=" N THR a 53 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'd' and resid 59 through 62 removed outlier: 3.853A pdb=" N THR d 71 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= AE, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= AF, first strand: chain 'n' and resid 33 through 35 removed outlier: 3.832A pdb=" N ASP n 33 " --> pdb=" O ASN n 98 " (cutoff:3.500A) 1438 hydrogen bonds defined for protein. 4020 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: 11.86 Time building geometry restraints manager: 14.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11486 1.34 - 1.46: 4778 1.46 - 1.58: 17926 1.58 - 1.69: 88 1.69 - 1.81: 324 Bond restraints: 34602 Sorted by residual: bond pdb=" C4 ADP G 601 " pdb=" C5 ADP G 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP q 601 " pdb=" C5 ADP q 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C4 ADP g 601 " pdb=" C5 ADP g 601 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C4 ADP Q 601 " pdb=" C5 ADP Q 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP Q 601 " pdb=" C6 ADP Q 601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 34597 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.81: 703 105.81 - 113.39: 20477 113.39 - 120.97: 16479 120.97 - 128.55: 9006 128.55 - 136.14: 215 Bond angle restraints: 46880 Sorted by residual: angle pdb=" C GLY q 122 " pdb=" N LEU q 123 " pdb=" CA LEU q 123 " ideal model delta sigma weight residual 121.64 107.49 14.15 2.13e+00 2.20e-01 4.42e+01 angle pdb=" C GLY Q 122 " pdb=" N LEU Q 123 " pdb=" CA LEU Q 123 " ideal model delta sigma weight residual 121.64 107.55 14.09 2.13e+00 2.20e-01 4.38e+01 angle pdb=" CA LYS D 497 " pdb=" CB LYS D 497 " pdb=" CG LYS D 497 " ideal model delta sigma weight residual 114.10 124.59 -10.49 2.00e+00 2.50e-01 2.75e+01 angle pdb=" CA LYS d 497 " pdb=" CB LYS d 497 " pdb=" CG LYS d 497 " ideal model delta sigma weight residual 114.10 124.55 -10.45 2.00e+00 2.50e-01 2.73e+01 angle pdb=" N GLN z 17 " pdb=" CA GLN z 17 " pdb=" C GLN z 17 " ideal model delta sigma weight residual 113.55 107.63 5.92 1.26e+00 6.30e-01 2.21e+01 ... (remaining 46875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 20480 35.79 - 71.57: 648 71.57 - 107.36: 50 107.36 - 143.14: 9 143.14 - 178.93: 13 Dihedral angle restraints: 21200 sinusoidal: 8362 harmonic: 12838 Sorted by residual: dihedral pdb=" O1B ADP G 601 " pdb=" O3A ADP G 601 " pdb=" PB ADP G 601 " pdb=" PA ADP G 601 " ideal model delta sinusoidal sigma weight residual -60.00 118.92 -178.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP d 602 " pdb=" O5' ADP d 602 " pdb=" PA ADP d 602 " pdb=" O2A ADP d 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.28 177.73 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 602 " pdb=" O5' ADP D 602 " pdb=" PA ADP D 602 " pdb=" O2A ADP D 602 " ideal model delta sinusoidal sigma weight residual 300.00 122.32 177.68 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 21197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4526 0.054 - 0.109: 992 0.109 - 0.163: 134 0.163 - 0.217: 30 0.217 - 0.272: 2 Chirality restraints: 5684 Sorted by residual: chirality pdb=" CB ILE e 507 " pdb=" CA ILE e 507 " pdb=" CG1 ILE e 507 " pdb=" CG2 ILE e 507 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE E 507 " pdb=" CA ILE E 507 " pdb=" CG1 ILE E 507 " pdb=" CG2 ILE E 507 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE b 51 " pdb=" CA ILE b 51 " pdb=" CG1 ILE b 51 " pdb=" CG2 ILE b 51 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5681 not shown) Planarity restraints: 5936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 101 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C SER B 101 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 101 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL B 102 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 89 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C LYS e 89 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS e 89 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU e 90 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 101 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER b 101 " -0.068 2.00e-02 2.50e+03 pdb=" O SER b 101 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL b 102 " 0.023 2.00e-02 2.50e+03 ... (remaining 5933 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 175 2.40 - 3.03: 21365 3.03 - 3.65: 51553 3.65 - 4.28: 80045 4.28 - 4.90: 133831 Nonbonded interactions: 286969 Sorted by model distance: nonbonded pdb=" O3A ADP Q 601 " pdb="MG MG Q 602 " model vdw 1.778 2.170 nonbonded pdb=" O3A ADP q 601 " pdb="MG MG q 602 " model vdw 1.804 2.170 nonbonded pdb="MG MG d 601 " pdb=" O1A ADP d 602 " model vdw 1.949 2.170 nonbonded pdb="MG MG D 601 " pdb=" O1A ADP D 602 " model vdw 1.950 2.170 nonbonded pdb=" O3A ADP h 601 " pdb="MG MG h 602 " model vdw 1.979 2.170 ... (remaining 286964 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' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'D' and (resid 28 through 34 or resid 36 through 538 or resid 601 through \ 602)) selection = (chain 'd' and (resid 28 through 34 or resid 36 through 538 or resid 601 through \ 602)) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.480 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 90.640 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.006 0.110 34602 Z= 0.369 Angle : 0.848 14.153 46880 Z= 0.435 Chirality : 0.046 0.272 5684 Planarity : 0.005 0.044 5936 Dihedral : 17.645 178.925 12876 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.01 % Rotamer: Outliers : 1.87 % Allowed : 18.12 % Favored : 80.01 % 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: -4.70 (0.10), residues: 4410 helix: -2.79 (0.08), residues: 2784 sheet: -2.71 (0.38), residues: 124 loop : -3.49 (0.12), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 109 HIS 0.010 0.001 HIS A 113 PHE 0.020 0.002 PHE q 445 TYR 0.014 0.001 TYR E 420 ARG 0.024 0.001 ARG a 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 942 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 GLU cc_start: 0.8147 (tp30) cc_final: 0.7869 (tp30) REVERT: E 426 GLU cc_start: 0.8488 (mp0) cc_final: 0.8260 (mp0) REVERT: E 501 MET cc_start: 0.8986 (mmp) cc_final: 0.8093 (mmt) REVERT: E 532 ASP cc_start: 0.7973 (t0) cc_final: 0.7650 (t0) REVERT: H 455 PHE cc_start: 0.8559 (m-10) cc_final: 0.8224 (m-10) REVERT: Q 52 MET cc_start: 0.8945 (mmm) cc_final: 0.8659 (mmm) REVERT: Q 85 MET cc_start: 0.8370 (mtm) cc_final: 0.7575 (mtt) REVERT: Q 113 GLU cc_start: 0.8018 (tt0) cc_final: 0.7729 (tt0) REVERT: Q 393 ASP cc_start: 0.7731 (t0) cc_final: 0.7497 (t0) REVERT: Z 79 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8833 (tttp) REVERT: Z 101 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7935 (mm-30) REVERT: Z 104 LYS cc_start: 0.9035 (tttt) cc_final: 0.8784 (tttm) REVERT: Z 170 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7923 (mm-30) REVERT: Z 498 TYR cc_start: 0.7824 (t80) cc_final: 0.7588 (t80) REVERT: Z 502 LYS cc_start: 0.8482 (tttt) cc_final: 0.8108 (ttpp) REVERT: G 21 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8119 (mmtt) REVERT: G 47 MET cc_start: 0.8686 (mmt) cc_final: 0.8103 (mmt) REVERT: G 90 GLU cc_start: 0.7659 (tp30) cc_final: 0.7446 (tp30) REVERT: G 104 GLU cc_start: 0.8178 (tp30) cc_final: 0.7945 (tp30) REVERT: G 110 GLU cc_start: 0.7655 (tm-30) cc_final: 0.6241 (tm-30) REVERT: G 114 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7224 (mt-10) REVERT: A 430 MET cc_start: 0.8252 (ttm) cc_final: 0.7782 (ttm) REVERT: D 39 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9148 (m) REVERT: D 57 MET cc_start: 0.8866 (mmm) cc_final: 0.8649 (mmp) REVERT: D 60 MET cc_start: 0.7851 (mtm) cc_final: 0.7538 (mtm) REVERT: D 479 GLU cc_start: 0.8111 (tp30) cc_final: 0.7897 (tp30) REVERT: D 483 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: B 94 GLU cc_start: 0.7899 (tt0) cc_final: 0.7092 (tm-30) REVERT: B 108 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7465 (mm-30) REVERT: B 112 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7404 (mp0) REVERT: B 120 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8524 (ttmm) REVERT: B 160 MET cc_start: 0.8869 (mmm) cc_final: 0.8669 (mmm) REVERT: B 414 GLU cc_start: 0.7894 (mp0) cc_final: 0.7553 (mp0) REVERT: e 39 MET cc_start: 0.8266 (tpp) cc_final: 0.8011 (mmm) REVERT: e 149 ASP cc_start: 0.7950 (p0) cc_final: 0.7727 (t70) REVERT: e 485 MET cc_start: 0.8173 (mmm) cc_final: 0.7959 (mpp) REVERT: e 486 ASN cc_start: 0.8548 (t0) cc_final: 0.8235 (t0) REVERT: e 489 LEU cc_start: 0.8651 (mp) cc_final: 0.8123 (mt) REVERT: e 522 GLN cc_start: 0.8242 (mt0) cc_final: 0.7911 (tt0) REVERT: q 52 MET cc_start: 0.8723 (mmm) cc_final: 0.8317 (mmm) REVERT: q 165 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7955 (mtp-110) REVERT: q 462 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7683 (mp0) REVERT: z 46 MET cc_start: 0.8379 (tpt) cc_final: 0.8015 (tpp) REVERT: z 62 VAL cc_start: 0.9358 (t) cc_final: 0.9092 (t) REVERT: z 79 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8793 (ttpp) REVERT: z 85 ASP cc_start: 0.7561 (p0) cc_final: 0.7162 (t0) REVERT: z 104 LYS cc_start: 0.8811 (tttt) cc_final: 0.8469 (tttp) REVERT: z 519 ASP cc_start: 0.8244 (m-30) cc_final: 0.7932 (m-30) REVERT: g 59 MET cc_start: 0.8235 (mtm) cc_final: 0.8030 (mtm) REVERT: g 83 ILE cc_start: 0.8829 (mm) cc_final: 0.8613 (mt) REVERT: g 110 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6303 (tm-30) REVERT: g 114 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7098 (mt-10) REVERT: g 115 GLN cc_start: 0.8777 (mt0) cc_final: 0.8514 (mt0) REVERT: g 489 ASP cc_start: 0.8546 (t0) cc_final: 0.8239 (t0) REVERT: g 491 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8196 (mttm) REVERT: a 17 ILE cc_start: 0.9096 (tt) cc_final: 0.8848 (mt) REVERT: a 42 ASP cc_start: 0.7873 (m-30) cc_final: 0.7656 (m-30) REVERT: a 82 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8409 (tm-30) REVERT: a 440 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8238 (mm-30) REVERT: a 450 ASN cc_start: 0.8792 (t0) cc_final: 0.8448 (t0) REVERT: d 39 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8545 (t) REVERT: d 118 ASP cc_start: 0.7846 (t0) cc_final: 0.7294 (t0) REVERT: d 479 GLU cc_start: 0.8143 (tp30) cc_final: 0.7584 (tp30) REVERT: d 483 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8229 (mmm-85) REVERT: d 534 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5893 (t70) REVERT: b 76 VAL cc_start: 0.8559 (t) cc_final: 0.8338 (m) REVERT: b 135 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8320 (ttmm) REVERT: b 390 LEU cc_start: 0.9014 (tp) cc_final: 0.8646 (tp) REVERT: b 441 LYS cc_start: 0.8556 (mttt) cc_final: 0.8291 (mtpp) REVERT: b 498 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7597 (mt0) REVERT: n 98 ASN cc_start: 0.6763 (t0) cc_final: 0.6369 (t0) outliers start: 68 outliers final: 17 residues processed: 989 average time/residue: 0.5108 time to fit residues: 790.9860 Evaluate side-chains 622 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 601 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 127 GLU Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain e residue 109 VAL Chi-restraints excluded: chain q residue 127 GLU Chi-restraints excluded: chain z residue 15 ARG Chi-restraints excluded: chain d residue 39 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 450 CYS Chi-restraints excluded: chain d residue 534 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-dev-5288/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-dev-5288/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: 74.6098 > 50: distance: 101 - 126: 34.136 distance: 107 - 131: 37.227 distance: 110 - 115: 35.147 distance: 111 - 138: 38.255 distance: 115 - 116: 40.530 distance: 116 - 117: 40.336 distance: 116 - 119: 68.435 distance: 117 - 118: 56.668 distance: 117 - 126: 39.183 distance: 118 - 143: 3.990 distance: 119 - 120: 70.633 distance: 120 - 121: 38.465 distance: 121 - 122: 56.470 distance: 122 - 123: 29.802 distance: 123 - 124: 46.858 distance: 123 - 125: 39.752 distance: 126 - 127: 57.734 distance: 127 - 128: 56.566 distance: 127 - 130: 56.776 distance: 128 - 129: 41.159 distance: 128 - 131: 68.867 distance: 129 - 152: 55.559 distance: 131 - 132: 56.265 distance: 132 - 133: 56.674 distance: 132 - 135: 26.983 distance: 133 - 134: 40.728 distance: 133 - 138: 39.680 distance: 135 - 136: 43.431 distance: 135 - 137: 27.399 distance: 138 - 139: 65.088 distance: 139 - 140: 32.227 distance: 139 - 142: 50.188 distance: 140 - 141: 55.894 distance: 140 - 143: 69.435 distance: 143 - 144: 39.011 distance: 144 - 145: 56.821 distance: 144 - 147: 69.315 distance: 145 - 152: 69.743 distance: 147 - 148: 56.433 distance: 148 - 149: 57.967 distance: 149 - 150: 39.117 distance: 149 - 151: 39.069 distance: 152 - 153: 39.859 distance: 153 - 156: 39.677 distance: 154 - 155: 56.791 distance: 154 - 157: 69.510 distance: 157 - 158: 57.462 distance: 158 - 159: 40.418 distance: 158 - 161: 39.837 distance: 159 - 160: 57.491 distance: 159 - 165: 39.784 distance: 161 - 162: 57.858 distance: 162 - 163: 40.923 distance: 162 - 164: 55.533 distance: 165 - 166: 56.470 distance: 166 - 169: 57.871 distance: 167 - 168: 56.388 distance: 167 - 174: 39.878 distance: 169 - 170: 56.885 distance: 170 - 171: 59.290 distance: 171 - 172: 57.343 distance: 171 - 173: 22.218 distance: 174 - 175: 57.780 distance: 175 - 176: 22.990 distance: 175 - 178: 68.678 distance: 176 - 177: 43.765 distance: 176 - 181: 38.867 distance: 177 - 203: 32.785 distance: 178 - 179: 49.056 distance: 178 - 180: 54.352 distance: 181 - 182: 40.964 distance: 182 - 183: 40.202 distance: 183 - 189: 35.286 distance: 184 - 209: 33.260 distance: 185 - 187: 55.003 distance: 186 - 188: 45.769