Starting phenix.real_space_refine on Tue Mar 19 22:10:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/03_2024/7v7n_31775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/03_2024/7v7n_31775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/03_2024/7v7n_31775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/03_2024/7v7n_31775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/03_2024/7v7n_31775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/03_2024/7v7n_31775.pdb" } resolution = 2.9 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= -0.002 sd= 0.038 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 108 5.16 5 C 16152 2.51 5 N 4139 2.21 5 O 5031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25430 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.31, per 1000 atoms: 0.52 Number of scatterers: 25430 At special positions: 0 Unit cell: (145.2, 148.5, 178.2, 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 108 16.00 O 5031 8.00 N 4139 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.02 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.02 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 329 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 329 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 341 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 232 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 16.10 Conformation dependent library (CDL) restraints added in 4.6 seconds 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 25.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.577A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 388 removed outlier: 4.522A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.921A pdb=" N VAL A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.672A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.976A pdb=" N THR A 636 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.645A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.502A pdb=" N LYS A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.779A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.186A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 4.009A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.119A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.685A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.039A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.793A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.712A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.638A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.975A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.567A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.647A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.364A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 removed outlier: 3.577A pdb=" N GLU C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.721A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.607A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.765A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.591A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.500A pdb=" N SER C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.962A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.712A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.578A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.633A pdb=" N GLY C 887 " --> pdb=" O TRP C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.931A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1032 removed outlier: 4.531A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.731A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.635A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.014A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.116A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.478A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 326 removed outlier: 5.097A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.590A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.041A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 701 removed outlier: 7.083A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.561A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.604A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.337A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.971A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.555A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.455A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.374A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.058A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.127A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.493A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 786 through 788 removed outlier: 5.745A pdb=" N ILE B 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.049A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 30 removed outlier: 8.391A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.919A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.069A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.582A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.892A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.212A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.810A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.598A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE9, first strand: chain 'C' and resid 1092 through 1095 993 hydrogen bonds defined for protein. 2709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.03 Time building geometry restraints manager: 16.64 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: 8014 1.34 - 1.46: 6436 1.46 - 1.58: 11402 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25984 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.89e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 25979 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.58: 685 106.58 - 113.43: 14623 113.43 - 120.28: 8802 120.28 - 127.13: 11033 127.13 - 133.98: 214 Bond angle restraints: 35357 Sorted by residual: angle pdb=" C CYS A 660 " pdb=" N ASP A 661 " pdb=" CA ASP A 661 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.45 -3.75 1.22e+00 6.72e-01 9.45e+00 angle pdb=" N VAL C 339 " pdb=" CA VAL C 339 " pdb=" C VAL C 339 " ideal model delta sigma weight residual 113.39 109.20 4.19 1.47e+00 4.63e-01 8.14e+00 angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 122.29 117.99 4.30 1.65e+00 3.67e-01 6.80e+00 angle pdb=" C VAL B 481 " pdb=" N GLU B 482 " pdb=" CA GLU B 482 " ideal model delta sigma weight residual 121.76 127.45 -5.69 2.19e+00 2.09e-01 6.76e+00 ... (remaining 35352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 15394 21.60 - 43.19: 988 43.19 - 64.79: 166 64.79 - 86.38: 41 86.38 - 107.98: 9 Dihedral angle restraints: 16598 sinusoidal: 7571 harmonic: 9027 Sorted by residual: dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -2.39 -83.61 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 536 " pdb=" SG CYS B 536 " pdb=" SG CYS B 588 " pdb=" CB CYS B 588 " ideal model delta sinusoidal sigma weight residual -86.00 -10.56 -75.44 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 536 " pdb=" SG CYS C 536 " pdb=" SG CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sinusoidal sigma weight residual -86.00 -11.49 -74.51 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 16595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4230 0.137 - 0.275: 26 0.275 - 0.412: 2 0.412 - 0.550: 1 0.550 - 0.687: 2 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 4258 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.027 2.00e-02 2.50e+03 2.51e-02 7.90e+00 pdb=" CG ASN B1072 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " -0.001 2.00e-02 2.50e+03 2.26e-02 6.36e+00 pdb=" CG ASN B 232 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 904 " -0.019 2.00e-02 2.50e+03 1.75e-02 5.36e+00 pdb=" CG PHE C 904 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 904 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 904 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 904 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 904 " -0.001 2.00e-02 2.50e+03 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1156 2.72 - 3.26: 25010 3.26 - 3.81: 39404 3.81 - 4.35: 45870 4.35 - 4.90: 81156 Nonbonded interactions: 192596 Sorted by model distance: nonbonded pdb=" OD1 ASP C 566 " pdb=" OG1 THR C 570 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.190 2.440 nonbonded pdb=" O GLU A 154 " pdb=" OH TYR A 158 " model vdw 2.195 2.440 nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.211 2.440 nonbonded pdb=" O ARG A 212 " pdb=" OH TYR A 264 " model vdw 2.212 2.440 ... (remaining 192591 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 14 through 619 or resid 631 through 1144 or resid 2001 thr \ ough 2004)) selection = (chain 'B' and (resid 14 through 825 or resid 852 through 1144 or resid 2001 thr \ ough 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 631 through 1144 or resid 2001 thr \ ough 2004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 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: 13.300 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 71.050 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25984 Z= 0.321 Angle : 0.620 8.008 35357 Z= 0.307 Chirality : 0.050 0.687 4261 Planarity : 0.004 0.043 4463 Dihedral : 13.977 107.980 10666 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.11 (0.15), residues: 3053 helix: 2.05 (0.22), residues: 646 sheet: 0.76 (0.19), residues: 721 loop : -1.08 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 884 HIS 0.003 0.001 HIS C1056 PHE 0.040 0.001 PHE C 904 TYR 0.019 0.001 TYR A 871 ARG 0.005 0.000 ARG C1037 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8171 (t0) cc_final: 0.7906 (t0) REVERT: B 415 LYS cc_start: 0.9143 (tptm) cc_final: 0.8836 (tppt) REVERT: C 416 ILE cc_start: 0.9070 (mp) cc_final: 0.8841 (pp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 1.1538 time to fit residues: 152.6249 Evaluate side-chains 72 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 66.7149 > 50: distance: 10 - 132: 18.192 distance: 22 - 121: 24.108 distance: 25 - 118: 25.095 distance: 37 - 44: 3.381 distance: 60 - 64: 23.467 distance: 64 - 65: 14.442 distance: 65 - 66: 32.677 distance: 65 - 68: 27.463 distance: 66 - 67: 43.658 distance: 66 - 71: 25.448 distance: 68 - 69: 24.005 distance: 68 - 70: 27.330 distance: 71 - 72: 8.991 distance: 72 - 73: 11.039 distance: 72 - 75: 16.782 distance: 73 - 74: 18.146 distance: 75 - 76: 7.213 distance: 75 - 77: 18.969 distance: 78 - 79: 5.555 distance: 79 - 80: 15.324 distance: 79 - 82: 23.599 distance: 80 - 81: 22.397 distance: 80 - 87: 10.136 distance: 82 - 83: 39.909 distance: 83 - 84: 19.132 distance: 84 - 85: 10.122 distance: 85 - 86: 4.689 distance: 87 - 88: 35.143 distance: 88 - 89: 29.898 distance: 88 - 91: 7.857 distance: 89 - 90: 46.841 distance: 89 - 98: 7.656 distance: 91 - 92: 14.518 distance: 92 - 93: 15.727 distance: 92 - 94: 16.053 distance: 93 - 95: 6.772 distance: 94 - 96: 13.146 distance: 95 - 97: 8.490 distance: 96 - 97: 11.190 distance: 98 - 99: 31.649 distance: 99 - 100: 25.986 distance: 99 - 102: 24.925 distance: 100 - 101: 24.665 distance: 100 - 106: 34.073 distance: 102 - 103: 38.392 distance: 103 - 104: 31.786 distance: 103 - 105: 28.127 distance: 106 - 107: 37.958 distance: 107 - 108: 57.296 distance: 108 - 109: 35.107 distance: 108 - 110: 17.216 distance: 110 - 111: 15.363 distance: 111 - 112: 25.205 distance: 111 - 114: 62.623 distance: 112 - 113: 48.313 distance: 112 - 118: 15.579 distance: 114 - 115: 17.613 distance: 115 - 116: 34.087 distance: 115 - 117: 32.654 distance: 118 - 119: 9.111 distance: 119 - 120: 30.643 distance: 119 - 122: 12.403 distance: 120 - 121: 12.012 distance: 120 - 125: 23.591 distance: 122 - 123: 49.203 distance: 122 - 124: 8.902 distance: 125 - 126: 12.358 distance: 126 - 127: 21.248 distance: 126 - 129: 10.689 distance: 127 - 128: 27.218 distance: 127 - 132: 38.344 distance: 129 - 130: 8.907 distance: 129 - 131: 19.027 distance: 132 - 133: 17.658 distance: 133 - 134: 26.493 distance: 133 - 136: 38.411 distance: 134 - 135: 51.419 distance: 134 - 140: 27.469 distance: 136 - 137: 24.328 distance: 137 - 138: 19.076 distance: 137 - 139: 10.557