Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 22:42:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/10_2023/7x08_32920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/10_2023/7x08_32920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/10_2023/7x08_32920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/10_2023/7x08_32920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/10_2023/7x08_32920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x08_32920/10_2023/7x08_32920_updated.pdb" } resolution = 2.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 159 5.16 5 C 23067 2.51 5 N 5970 2.21 5 O 7200 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 ARG 78": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 207": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "M GLU 164": "OE1" <-> "OE2" Residue "M GLU 187": "OE1" <-> "OE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "N GLU 164": "OE1" <-> "OE2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "N GLU 207": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 36396 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "L" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "I" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "M" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "J" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1550 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 180 Unusual residues: {'EIC': 2, 'NAG': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 18.86, per 1000 atoms: 0.52 Number of scatterers: 36396 At special positions: 0 Unit cell: (185.877, 197.834, 217.4, 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 159 16.00 O 7200 8.00 N 5970 7.00 C 23067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.78 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.92 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.49 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.78 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.49 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=1.78 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.94 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.99 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 149 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 138 " - pdb=" SG CYS M 197 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 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-ASN " NAG A1403 " - " ASN A 61 " " NAG A1404 " - " ASN A 122 " " NAG A1405 " - " ASN A 149 " " NAG A1406 " - " ASN A 165 " " NAG A1407 " - " ASN A 234 " " NAG A1408 " - " ASN A 282 " " NAG A1409 " - " ASN A 343 " " NAG A1410 " - " ASN A 603 " " NAG A1413 " - " ASN A 657 " " NAG A1414 " - " ASN A 709 " " NAG B1403 " - " ASN B 61 " " NAG B1404 " - " ASN B 122 " " NAG B1405 " - " ASN B 149 " " NAG B1406 " - " ASN B 165 " " NAG B1407 " - " ASN B 234 " " NAG B1408 " - " ASN B 282 " " NAG B1409 " - " ASN B 343 " " NAG B1410 " - " ASN B 603 " " NAG B1413 " - " ASN B 657 " " NAG B1414 " - " ASN B 709 " " NAG C1403 " - " ASN C 61 " " NAG C1404 " - " ASN C 122 " " NAG C1405 " - " ASN C 149 " " NAG C1406 " - " ASN C 165 " " NAG C1407 " - " ASN C 234 " " NAG C1408 " - " ASN C 282 " " NAG C1409 " - " ASN C 343 " " NAG C1410 " - " ASN C 603 " " NAG C1413 " - " ASN C 657 " " NAG C1414 " - " ASN C 709 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN C 331 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN A 17 " " NAG U 1 " - " ASN A 616 " " NAG V 1 " - " ASN A 801 " " NAG W 1 " - " ASN A1134 " " NAG X 1 " - " ASN B 17 " " NAG Y 1 " - " ASN B 616 " " NAG Z 1 " - " ASN B 801 " " NAG a 1 " - " ASN B1074 " " NAG b 1 " - " ASN B1134 " " NAG c 1 " - " ASN C 17 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1074 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 5.2 seconds 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 63 sheets defined 15.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.57 Creating SS restraints... Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.835A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.089A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.764A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 421' 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 738 through 742 Processing helix chain 'A' and resid 747 through 755 removed outlier: 3.782A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 3.785A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.512A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.098A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.476A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.834A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.763A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 421' Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.785A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.510A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.098A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 981 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1145 Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.834A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 389' Processing helix chain 'C' and resid 405 through 409 removed outlier: 4.089A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.763A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 421' Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.781A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 removed outlier: 3.786A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 837 through 840 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.711A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.665A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.512A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.099A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.477A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'M' and resid 186 through 191 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'N' and resid 126 through 130 Processing helix chain 'N' and resid 186 through 191 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.208A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.490A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.688A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= N, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.207A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.897A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.756A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 242 through 247 removed outlier: 6.110A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.656A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.007A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= V, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.491A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.688A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.051A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AA, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.207A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 242 through 247 removed outlier: 6.109A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.655A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.006A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.522A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AI, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.489A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.687A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.599A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AN, first strand: chain 'H' and resid 17 through 23 Processing sheet with id= AO, first strand: chain 'H' and resid 116 through 118 removed outlier: 5.542A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.990A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 159 through 163 Processing sheet with id= AR, first strand: chain 'L' and resid 17 through 21 Processing sheet with id= AS, first strand: chain 'L' and resid 90 through 92 removed outlier: 6.566A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 118 through 122 Processing sheet with id= AU, first strand: chain 'L' and resid 149 through 153 Processing sheet with id= AV, first strand: chain 'I' and resid 17 through 23 Processing sheet with id= AW, first strand: chain 'I' and resid 116 through 118 removed outlier: 5.541A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 129 through 133 removed outlier: 5.990A pdb=" N TYR I 185 " --> pdb=" O ASP I 153 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 159 through 163 Processing sheet with id= AZ, first strand: chain 'M' and resid 17 through 21 Processing sheet with id= BA, first strand: chain 'M' and resid 90 through 92 removed outlier: 6.566A pdb=" N GLN M 39 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU M 48 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'M' and resid 118 through 122 Processing sheet with id= BC, first strand: chain 'M' and resid 149 through 153 Processing sheet with id= BD, first strand: chain 'J' and resid 17 through 23 Processing sheet with id= BE, first strand: chain 'J' and resid 116 through 118 removed outlier: 5.540A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.989A pdb=" N TYR J 185 " --> pdb=" O ASP J 153 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'J' and resid 159 through 163 Processing sheet with id= BH, first strand: chain 'N' and resid 17 through 21 Processing sheet with id= BI, first strand: chain 'N' and resid 90 through 92 removed outlier: 6.566A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'N' and resid 118 through 122 Processing sheet with id= BK, first strand: chain 'N' and resid 149 through 153 1224 hydrogen bonds defined for protein. 3393 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: 18.62 Time building geometry restraints manager: 16.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11335 1.34 - 1.46: 9285 1.46 - 1.59: 16406 1.59 - 1.71: 0 1.71 - 1.84: 204 Bond restraints: 37230 Sorted by residual: bond pdb=" C GLY A 891 " pdb=" N PRO A 892 " ideal model delta sigma weight residual 1.329 1.390 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.26e-02 6.30e+03 2.21e+01 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.32e-02 5.74e+03 1.96e+01 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.318 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.318 0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 37225 not shown) Histogram of bond angle deviations from ideal: 99.68 - 107.51: 1589 107.51 - 115.35: 22433 115.35 - 123.18: 24312 123.18 - 131.01: 2212 131.01 - 138.85: 112 Bond angle restraints: 50658 Sorted by residual: angle pdb=" N VAL J 63 " pdb=" CA VAL J 63 " pdb=" C VAL J 63 " ideal model delta sigma weight residual 113.71 106.15 7.56 9.50e-01 1.11e+00 6.33e+01 angle pdb=" N VAL I 63 " pdb=" CA VAL I 63 " pdb=" C VAL I 63 " ideal model delta sigma weight residual 113.71 106.17 7.54 9.50e-01 1.11e+00 6.31e+01 angle pdb=" N VAL H 63 " pdb=" CA VAL H 63 " pdb=" C VAL H 63 " ideal model delta sigma weight residual 113.71 106.18 7.53 9.50e-01 1.11e+00 6.28e+01 angle pdb=" C GLY A 891 " pdb=" N PRO A 892 " pdb=" CA PRO A 892 " ideal model delta sigma weight residual 120.14 114.12 6.02 1.06e+00 8.90e-01 3.22e+01 angle pdb=" N LEU C 517 " pdb=" CA LEU C 517 " pdb=" C LEU C 517 " ideal model delta sigma weight residual 109.24 117.77 -8.53 1.51e+00 4.39e-01 3.19e+01 ... (remaining 50653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 18713 17.56 - 35.11: 1973 35.11 - 52.67: 636 52.67 - 70.22: 213 70.22 - 87.78: 44 Dihedral angle restraints: 21579 sinusoidal: 8349 harmonic: 13230 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.57 80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 21576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 5892 0.305 - 0.609: 11 0.609 - 0.914: 13 0.914 - 1.218: 9 1.218 - 1.523: 9 Chirality restraints: 5934 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.50e+03 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.40 1.00 2.00e-02 2.50e+03 2.49e+03 ... (remaining 5931 not shown) Planarity restraints: 6495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN B 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN B 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG B1413 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN C 657 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " -0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.577 2.00e-02 2.50e+03 pdb=" C1 NAG C1413 " -0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.197 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" CG ASN A 657 " -0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.091 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.577 2.00e-02 2.50e+03 pdb=" C1 NAG A1413 " 0.391 2.00e-02 2.50e+03 ... (remaining 6492 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 262 2.51 - 3.11: 25861 3.11 - 3.70: 52411 3.70 - 4.30: 78788 4.30 - 4.90: 133082 Nonbonded interactions: 290404 Sorted by model distance: nonbonded pdb=" O SER B 940 " pdb=" OG1 THR B 941 " model vdw 1.910 2.440 nonbonded pdb=" O SER C 940 " pdb=" OG1 THR C 941 " model vdw 1.910 2.440 nonbonded pdb=" O SER A 940 " pdb=" OG1 THR A 941 " model vdw 1.911 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.195 2.440 ... (remaining 290399 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 1146 or resid 1403 through 1414)) selection = (chain 'B' and (resid 14 through 1146 or resid 1403 through 1414)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.580 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: 0.030 Extract box with map and model: 7.720 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 97.790 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.640 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.009 0.088 37230 Z= 0.571 Angle : 0.965 13.845 50658 Z= 0.548 Chirality : 0.098 1.523 5934 Planarity : 0.010 0.279 6441 Dihedral : 17.172 87.781 12930 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.41 % Favored : 90.64 % Rotamer: Outliers : 10.68 % Allowed : 15.40 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.11), residues: 4530 helix: -0.87 (0.18), residues: 741 sheet: -0.82 (0.13), residues: 1317 loop : -2.84 (0.10), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9060 Ramachandran restraints generated. 4530 Oldfield, 0 Emsley, 4530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 507 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 421 outliers final: 50 residues processed: 824 average time/residue: 1.1899 time to fit residues: 1234.0054 Evaluate side-chains 314 residues out of total 3942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 264 time to evaluate : 4.130 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 0.3864 time to fit residues: 8.1552 ------------------------------------------------------------------------------- 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-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 67.9304 > 50: distance: 57 - 189: 27.461 distance: 70 - 178: 24.443 distance: 73 - 175: 21.343 distance: 123 - 144: 31.801 distance: 137 - 144: 35.407 distance: 144 - 145: 30.211 distance: 145 - 146: 53.491 distance: 145 - 148: 39.628 distance: 146 - 147: 38.743 distance: 146 - 155: 50.324 distance: 148 - 149: 44.128 distance: 149 - 150: 10.736 distance: 149 - 151: 29.964 distance: 150 - 152: 25.209 distance: 151 - 153: 46.893 distance: 152 - 154: 28.197 distance: 153 - 154: 33.267 distance: 155 - 156: 40.569 distance: 156 - 157: 32.301 distance: 156 - 159: 25.307 distance: 157 - 158: 36.938 distance: 157 - 163: 24.654 distance: 159 - 160: 48.170 distance: 160 - 161: 36.080 distance: 160 - 162: 34.970 distance: 163 - 164: 27.765 distance: 164 - 165: 34.507 distance: 165 - 166: 31.008 distance: 165 - 167: 53.501 distance: 167 - 168: 54.141 distance: 168 - 169: 62.055 distance: 168 - 171: 34.462 distance: 169 - 170: 58.229 distance: 169 - 175: 45.340 distance: 171 - 172: 26.325 distance: 172 - 173: 36.203 distance: 172 - 174: 39.043 distance: 175 - 176: 33.590 distance: 176 - 177: 37.934 distance: 176 - 179: 31.708 distance: 177 - 178: 45.526 distance: 177 - 182: 46.858 distance: 179 - 180: 31.074 distance: 179 - 181: 43.643 distance: 182 - 183: 43.909 distance: 183 - 184: 53.644 distance: 183 - 186: 23.561 distance: 184 - 185: 54.534 distance: 184 - 189: 21.226 distance: 186 - 187: 45.639 distance: 186 - 188: 17.753 distance: 189 - 190: 37.330 distance: 190 - 191: 28.267 distance: 190 - 193: 33.326 distance: 191 - 192: 34.265 distance: 191 - 197: 13.177 distance: 193 - 194: 22.979 distance: 194 - 195: 40.604 distance: 194 - 196: 30.698 distance: 197 - 198: 41.561 distance: 197 - 203: 38.688 distance: 198 - 199: 67.930 distance: 198 - 201: 53.128 distance: 199 - 200: 56.139 distance: 199 - 204: 57.850 distance: 201 - 202: 30.569 distance: 202 - 203: 63.317 distance: 204 - 205: 40.478 distance: 205 - 206: 56.844 distance: 205 - 208: 39.313 distance: 206 - 207: 28.450 distance: 206 - 211: 42.060 distance: 211 - 212: 43.039 distance: 212 - 213: 32.567 distance: 212 - 215: 30.297 distance: 213 - 214: 10.862 distance: 213 - 219: 19.814 distance: 215 - 216: 22.520 distance: 216 - 217: 22.896 distance: 216 - 218: 26.735 distance: 229 - 234: 3.059