Starting phenix.real_space_refine on Thu Mar 21 18:14:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epx_31249/03_2024/7epx_31249.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epx_31249/03_2024/7epx_31249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epx_31249/03_2024/7epx_31249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epx_31249/03_2024/7epx_31249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epx_31249/03_2024/7epx_31249.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7epx_31249/03_2024/7epx_31249.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 19542 2.51 5 N 5052 2.21 5 O 6124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L GLU 206": "OE1" <-> "OE2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 163": "OE1" <-> "OE2" Residue "M GLU 186": "OE1" <-> "OE2" Residue "M GLU 206": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30846 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 53, 'TRANS': 953} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 51, 'TRANS': 919} Chain breaks: 9 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1701 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "L" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "I" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1701 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "M" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 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 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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.33, per 1000 atoms: 0.53 Number of scatterers: 30846 At special positions: 0 Unit cell: (189.138, 173.92, 194.573, 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 128 16.00 O 6124 8.00 N 5052 7.00 C 19542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.15 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.96 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 137 " - pdb=" SG CYS M 196 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN B1074 " Time building additional restraints: 11.69 Conformation dependent library (CDL) restraints added in 5.1 seconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7192 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 19.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.064A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.567A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.577A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.864A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.064A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.568A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.565A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.246A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.568A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.699A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.623A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'L' and resid 124 through 130 Processing helix chain 'L' and resid 184 through 191 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'M' and resid 124 through 130 Processing helix chain 'M' and resid 184 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.081A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.720A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.369A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 319 removed outlier: 6.141A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.026A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.608A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.197A pdb=" N GLY H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.008A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.008A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AF4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.370A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN L 35 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 117 through 121 Processing sheet with id=AF7, first strand: chain 'L' and resid 117 through 121 Processing sheet with id=AF8, first strand: chain 'L' and resid 157 through 158 removed outlier: 4.439A pdb=" N TRP L 151 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.197A pdb=" N GLY I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 164 through 168 Processing sheet with id=AG5, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG6, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.370A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN M 35 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 117 through 121 Processing sheet with id=AG8, first strand: chain 'M' and resid 117 through 121 Processing sheet with id=AG9, first strand: chain 'M' and resid 157 through 158 removed outlier: 4.440A pdb=" N TRP M 151 " --> pdb=" O VAL M 158 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3108 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: 13.03 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8179 1.33 - 1.46: 8454 1.46 - 1.58: 14739 1.58 - 1.71: 0 1.71 - 1.84: 161 Bond restraints: 31533 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.25e+01 bond pdb=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.18e-02 7.18e+03 2.57e+01 bond pdb=" C GLN C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.31e-02 5.83e+03 2.08e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.89e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 ... (remaining 31528 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.74: 742 105.74 - 113.98: 18409 113.98 - 122.22: 18051 122.22 - 130.46: 5624 130.46 - 138.70: 101 Bond angle restraints: 42927 Sorted by residual: angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.09 6.29 1.03e+00 9.43e-01 3.72e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C GLN C 321 " pdb=" N PRO C 322 " pdb=" CA PRO C 322 " ideal model delta sigma weight residual 119.85 114.08 5.77 1.01e+00 9.80e-01 3.27e+01 ... (remaining 42922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16971 17.93 - 35.86: 1951 35.86 - 53.79: 608 53.79 - 71.72: 160 71.72 - 89.65: 48 Dihedral angle restraints: 19738 sinusoidal: 8548 harmonic: 11190 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5067 0.329 - 0.659: 4 0.659 - 0.988: 5 0.988 - 1.317: 0 1.317 - 1.647: 1 Chirality restraints: 5077 Sorted by residual: 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 -3.08 0.68 2.00e-02 2.50e+03 1.16e+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 -1.76 -0.64 2.00e-02 2.50e+03 1.02e+03 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 ... (remaining 5074 not shown) Planarity restraints: 5509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.104 2.00e-02 2.50e+03 1.98e-01 4.90e+02 pdb=" CG ASN C 331 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.355 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.141 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" CG ASN B 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.278 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.131 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN A 331 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.270 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.192 2.00e-02 2.50e+03 ... (remaining 5506 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 315 2.53 - 3.12: 23040 3.12 - 3.71: 45182 3.71 - 4.31: 66002 4.31 - 4.90: 109745 Nonbonded interactions: 244284 Sorted by model distance: nonbonded pdb=" O VAL H 125 " pdb=" OG SER H 126 " model vdw 1.934 2.440 nonbonded pdb=" O VAL I 125 " pdb=" OG SER I 126 " model vdw 1.934 2.440 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 1.966 2.520 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.140 2.520 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 ... (remaining 244279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 455 or resid 491 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1408)) selection = (chain 'B' and (resid 27 through 455 or resid 491 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' 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' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = 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: 1.450 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: 6.560 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 80.300 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.400 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.011 0.117 31533 Z= 0.685 Angle : 1.030 13.696 42927 Z= 0.590 Chirality : 0.072 1.647 5077 Planarity : 0.007 0.090 5461 Dihedral : 17.351 89.648 12408 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 2.40 % Allowed : 10.93 % Favored : 86.68 % Rotamer: Outliers : 10.46 % Allowed : 18.18 % Favored : 71.36 % 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: -3.96 (0.11), residues: 3798 helix: -2.43 (0.15), residues: 712 sheet: -1.64 (0.14), residues: 1053 loop : -3.36 (0.11), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 104 HIS 0.010 0.002 HIS H 32 PHE 0.033 0.003 PHE H 29 TYR 0.028 0.003 TYR B1067 ARG 0.007 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 359 time to evaluate : 2.883 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: A 109 THR cc_start: 0.5565 (OUTLIER) cc_final: 0.5314 (m) REVERT: A 130 VAL cc_start: 0.5994 (t) cc_final: 0.5765 (t) REVERT: A 143 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6436 (t) REVERT: A 335 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4914 (mp) REVERT: A 983 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7424 (mtm110) REVERT: A 1039 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8890 (mtp180) REVERT: B 109 THR cc_start: 0.6101 (OUTLIER) cc_final: 0.5748 (m) REVERT: B 153 MET cc_start: 0.4251 (mpp) cc_final: 0.2476 (ptt) REVERT: B 164 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.3161 (m-40) REVERT: B 422 ASN cc_start: 0.0201 (OUTLIER) cc_final: -0.0137 (t0) REVERT: B 950 ASP cc_start: 0.7990 (m-30) cc_final: 0.7785 (m-30) REVERT: C 153 MET cc_start: 0.3196 (mpp) cc_final: 0.1237 (ptm) REVERT: C 158 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.4531 (ttp-170) REVERT: C 218 GLN cc_start: 0.7063 (tt0) cc_final: 0.6663 (tm130) REVERT: C 314 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: C 528 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6511 (mmmm) REVERT: C 529 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6757 (ptmm) REVERT: C 535 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7756 (ttmt) REVERT: H 83 MET cc_start: -0.0818 (mtp) cc_final: -0.1414 (mmm) REVERT: H 114 MET cc_start: 0.0113 (mtm) cc_final: -0.0129 (mtp) REVERT: H 178 HIS cc_start: 0.0303 (OUTLIER) cc_final: -0.0230 (m-70) REVERT: I 102 TYR cc_start: 0.2377 (OUTLIER) cc_final: 0.2136 (p90) REVERT: I 211 ASN cc_start: 0.0918 (OUTLIER) cc_final: 0.0582 (m110) REVERT: M 183 LEU cc_start: 0.0426 (OUTLIER) cc_final: -0.0509 (tp) outliers start: 351 outliers final: 75 residues processed: 654 average time/residue: 1.0365 time to fit residues: 832.1635 Evaluate side-chains 261 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 169 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 239 GLN A 317 ASN A 450 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 960 ASN A 969 ASN A 992 GLN A1101 HIS B 134 GLN B 137 ASN B 317 ASN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 675 GLN B 690 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 935 GLN B 992 GLN B1002 GLN B1005 GLN B1054 GLN C 134 GLN C 137 ASN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1005 GLN C1071 GLN C1101 HIS L 6 GLN L 38 GLN L 191 HIS L 197 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 38 GLN M 191 HIS ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31533 Z= 0.288 Angle : 0.775 12.224 42927 Z= 0.384 Chirality : 0.051 0.532 5077 Planarity : 0.006 0.064 5461 Dihedral : 10.021 86.069 5759 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.66 % Favored : 91.13 % Rotamer: Outliers : 6.05 % Allowed : 22.03 % Favored : 71.92 % 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: -2.65 (0.12), residues: 3798 helix: -0.49 (0.19), residues: 710 sheet: -1.03 (0.15), residues: 1065 loop : -2.73 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 104 HIS 0.007 0.001 HIS M 191 PHE 0.017 0.002 PHE B 86 TYR 0.023 0.002 TYR H 102 ARG 0.004 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 182 time to evaluate : 3.340 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: A 335 LEU cc_start: 0.5278 (OUTLIER) cc_final: 0.4932 (mp) REVERT: A 546 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6402 (mm) REVERT: A 855 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.5633 (t80) REVERT: A 1094 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8777 (t) REVERT: B 153 MET cc_start: 0.4127 (mpp) cc_final: 0.2400 (ptt) REVERT: B 164 ASN cc_start: 0.4284 (OUTLIER) cc_final: 0.3345 (m-40) REVERT: B 554 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5938 (tp30) REVERT: B 1142 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7177 (tp-100) REVERT: C 153 MET cc_start: 0.2923 (mpp) cc_final: 0.0783 (ptm) REVERT: C 158 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.4603 (ttt180) REVERT: C 190 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7251 (mtm180) REVERT: C 537 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7749 (mtmm) REVERT: C 1129 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8985 (t) REVERT: H 34 MET cc_start: 0.4954 (mpm) cc_final: 0.4339 (mpm) REVERT: H 83 MET cc_start: -0.1334 (mtp) cc_final: -0.1768 (mmm) REVERT: H 114 MET cc_start: -0.0536 (mtm) cc_final: -0.0844 (mtp) REVERT: H 178 HIS cc_start: 0.0430 (OUTLIER) cc_final: -0.0128 (m-70) REVERT: L 192 ARG cc_start: -0.0074 (OUTLIER) cc_final: -0.0776 (tpt170) REVERT: I 83 MET cc_start: 0.2910 (mmp) cc_final: 0.1447 (mtp) REVERT: I 106 ASP cc_start: 0.4058 (OUTLIER) cc_final: 0.3551 (m-30) REVERT: I 184 LEU cc_start: 0.3005 (OUTLIER) cc_final: 0.2628 (pt) REVERT: I 211 ASN cc_start: 0.1058 (OUTLIER) cc_final: 0.0656 (m110) outliers start: 203 outliers final: 68 residues processed: 358 average time/residue: 0.9980 time to fit residues: 448.0669 Evaluate side-chains 230 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 146 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 192 ARG Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 289 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 348 optimal weight: 30.0000 chunk 376 optimal weight: 30.0000 chunk 310 optimal weight: 50.0000 chunk 345 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1011 GLN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 675 GLN B 804 GLN B1010 GLN C 218 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 544 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 935 GLN L 53 ASN ** L 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31533 Z= 0.254 Angle : 0.705 10.233 42927 Z= 0.344 Chirality : 0.049 0.712 5077 Planarity : 0.005 0.052 5461 Dihedral : 8.618 97.676 5666 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.43 % Favored : 91.39 % Rotamer: Outliers : 5.72 % Allowed : 22.53 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3798 helix: 0.22 (0.20), residues: 712 sheet: -0.58 (0.15), residues: 1068 loop : -2.39 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS C 49 PHE 0.022 0.002 PHE A 238 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 157 time to evaluate : 3.252 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: A 379 CYS cc_start: 0.1611 (OUTLIER) cc_final: 0.0465 (p) REVERT: A 546 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6436 (mm) REVERT: A 855 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5363 (t80) REVERT: A 1094 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (t) REVERT: B 153 MET cc_start: 0.3832 (mpp) cc_final: 0.2246 (ptt) REVERT: B 164 ASN cc_start: 0.3992 (OUTLIER) cc_final: 0.3231 (m-40) REVERT: B 554 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5820 (tp30) REVERT: B 900 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8286 (mtm) REVERT: B 957 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 1142 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7240 (tp-100) REVERT: C 153 MET cc_start: 0.2650 (mpp) cc_final: 0.0535 (ptm) REVERT: C 190 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7246 (mtm180) REVERT: H 83 MET cc_start: -0.1609 (mtp) cc_final: -0.1887 (mmm) REVERT: H 114 MET cc_start: -0.0778 (mtm) cc_final: -0.1084 (mtp) REVERT: H 178 HIS cc_start: 0.0531 (OUTLIER) cc_final: -0.0025 (m-70) REVERT: I 83 MET cc_start: 0.3275 (mmp) cc_final: 0.2201 (mtp) REVERT: I 106 ASP cc_start: 0.3793 (OUTLIER) cc_final: 0.3525 (m-30) REVERT: I 184 LEU cc_start: 0.2902 (OUTLIER) cc_final: 0.2468 (pt) REVERT: M 183 LEU cc_start: -0.0054 (OUTLIER) cc_final: -0.0918 (tp) outliers start: 192 outliers final: 76 residues processed: 324 average time/residue: 0.9636 time to fit residues: 396.2015 Evaluate side-chains 216 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 128 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain H residue 193 SER Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 233 optimal weight: 0.6980 chunk 349 optimal weight: 40.0000 chunk 370 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN L 53 ASN ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31533 Z= 0.333 Angle : 0.729 11.210 42927 Z= 0.354 Chirality : 0.051 0.878 5077 Planarity : 0.005 0.053 5461 Dihedral : 8.239 93.088 5641 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.00 % Favored : 91.81 % Rotamer: Outliers : 5.75 % Allowed : 22.38 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3798 helix: 0.39 (0.20), residues: 711 sheet: -0.44 (0.15), residues: 1052 loop : -2.25 (0.12), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 36 HIS 0.005 0.001 HIS B1048 PHE 0.020 0.002 PHE A 140 TYR 0.021 0.001 TYR B1067 ARG 0.010 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 141 time to evaluate : 3.314 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: A 333 THR cc_start: 0.5394 (OUTLIER) cc_final: 0.5087 (t) REVERT: A 379 CYS cc_start: 0.1490 (OUTLIER) cc_final: 0.0433 (p) REVERT: A 546 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6424 (mm) REVERT: A 855 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.5685 (t80) REVERT: A 869 MET cc_start: 0.8874 (mtt) cc_final: 0.8559 (mtt) REVERT: A 1094 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8853 (t) REVERT: B 153 MET cc_start: 0.3846 (mpp) cc_final: 0.2311 (pp-130) REVERT: B 164 ASN cc_start: 0.4008 (OUTLIER) cc_final: 0.3144 (m-40) REVERT: B 554 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6031 (tp30) REVERT: B 861 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9083 (mt) REVERT: B 900 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: B 933 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8236 (mtpt) REVERT: B 957 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 1142 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7418 (tp-100) REVERT: C 153 MET cc_start: 0.2883 (mpp) cc_final: 0.0447 (ttp) REVERT: C 190 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7343 (mtm180) REVERT: C 336 CYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5994 (t) REVERT: C 535 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7443 (ttmt) REVERT: H 60 TYR cc_start: 0.2235 (OUTLIER) cc_final: 0.1617 (m-10) REVERT: H 83 MET cc_start: -0.1081 (mtp) cc_final: -0.1503 (mmm) REVERT: H 114 MET cc_start: -0.1157 (mtm) cc_final: -0.1460 (mtp) REVERT: H 178 HIS cc_start: 0.0524 (OUTLIER) cc_final: 0.0082 (m-70) REVERT: I 34 MET cc_start: 0.4326 (OUTLIER) cc_final: 0.3145 (mpt) REVERT: I 106 ASP cc_start: 0.4133 (OUTLIER) cc_final: 0.3617 (m-30) REVERT: I 184 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2417 (pt) REVERT: M 183 LEU cc_start: -0.0144 (OUTLIER) cc_final: -0.1006 (tp) REVERT: M 195 SER cc_start: 0.2498 (OUTLIER) cc_final: 0.2190 (m) outliers start: 193 outliers final: 96 residues processed: 306 average time/residue: 0.8931 time to fit residues: 352.0725 Evaluate side-chains 239 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 123 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 275 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 332 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 53 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31533 Z= 0.169 Angle : 0.648 10.423 42927 Z= 0.312 Chirality : 0.047 0.704 5077 Planarity : 0.004 0.052 5461 Dihedral : 7.765 98.669 5640 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.00 % Favored : 92.81 % Rotamer: Outliers : 4.50 % Allowed : 23.90 % Favored : 71.59 % 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: -1.35 (0.13), residues: 3798 helix: 0.88 (0.20), residues: 706 sheet: -0.16 (0.15), residues: 1072 loop : -2.04 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 151 HIS 0.003 0.001 HIS I 35 PHE 0.018 0.001 PHE A 140 TYR 0.016 0.001 TYR B1067 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 144 time to evaluate : 3.163 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: A 333 THR cc_start: 0.5554 (OUTLIER) cc_final: 0.5243 (t) REVERT: A 389 ASP cc_start: 0.3937 (OUTLIER) cc_final: 0.3594 (p0) REVERT: A 546 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6363 (mm) REVERT: A 869 MET cc_start: 0.8812 (mtt) cc_final: 0.8498 (mtt) REVERT: A 1094 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (t) REVERT: B 153 MET cc_start: 0.3860 (mpp) cc_final: 0.2310 (pp-130) REVERT: B 164 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.2749 (p0) REVERT: B 554 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5954 (tp30) REVERT: B 900 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8284 (mtm) REVERT: B 957 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7460 (tm-30) REVERT: C 153 MET cc_start: 0.2966 (mpp) cc_final: 0.0547 (ttp) REVERT: H 83 MET cc_start: -0.1038 (mtp) cc_final: -0.1430 (mmm) REVERT: H 114 MET cc_start: -0.1407 (mtm) cc_final: -0.1684 (mtp) REVERT: H 178 HIS cc_start: 0.0512 (OUTLIER) cc_final: 0.0074 (m-70) REVERT: I 34 MET cc_start: 0.4267 (OUTLIER) cc_final: 0.3083 (mpt) REVERT: I 83 MET cc_start: 0.3183 (mmp) cc_final: 0.2146 (mtp) REVERT: I 106 ASP cc_start: 0.4240 (OUTLIER) cc_final: 0.3655 (m-30) REVERT: I 184 LEU cc_start: 0.2947 (OUTLIER) cc_final: 0.2388 (pt) REVERT: I 211 ASN cc_start: 0.1703 (OUTLIER) cc_final: 0.1427 (m110) REVERT: M 136 VAL cc_start: 0.1082 (OUTLIER) cc_final: 0.0825 (m) outliers start: 151 outliers final: 71 residues processed: 273 average time/residue: 0.9101 time to fit residues: 320.2129 Evaluate side-chains 203 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 119 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 5.9990 chunk 333 optimal weight: 50.0000 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 307 optimal weight: 40.0000 chunk 171 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 99 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31533 Z= 0.303 Angle : 0.684 10.484 42927 Z= 0.331 Chirality : 0.050 0.808 5077 Planarity : 0.005 0.051 5461 Dihedral : 7.703 99.223 5636 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.66 % Favored : 92.15 % Rotamer: Outliers : 4.89 % Allowed : 24.08 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3798 helix: 0.84 (0.20), residues: 706 sheet: -0.17 (0.15), residues: 1061 loop : -1.98 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.021 0.002 PHE B 238 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 135 time to evaluate : 3.672 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: A 333 THR cc_start: 0.5398 (OUTLIER) cc_final: 0.5093 (t) REVERT: A 379 CYS cc_start: 0.1419 (OUTLIER) cc_final: 0.0325 (p) REVERT: A 389 ASP cc_start: 0.4193 (OUTLIER) cc_final: 0.3841 (p0) REVERT: A 546 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6279 (mm) REVERT: A 855 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5571 (t80) REVERT: A 869 MET cc_start: 0.8851 (mtt) cc_final: 0.8552 (mtt) REVERT: A 1094 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8823 (t) REVERT: A 1113 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: B 153 MET cc_start: 0.3682 (mpp) cc_final: 0.2204 (pp-130) REVERT: B 164 ASN cc_start: 0.3961 (OUTLIER) cc_final: 0.2922 (p0) REVERT: B 427 ASP cc_start: 0.1157 (OUTLIER) cc_final: 0.0637 (t70) REVERT: B 554 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6040 (tp30) REVERT: B 861 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9090 (mt) REVERT: B 900 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8259 (mtm) REVERT: B 957 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 994 ASP cc_start: 0.7355 (t70) cc_final: 0.7135 (t0) REVERT: C 153 MET cc_start: 0.2156 (mpp) cc_final: 0.0231 (ttp) REVERT: C 233 ILE cc_start: 0.7177 (OUTLIER) cc_final: 0.6877 (tp) REVERT: H 60 TYR cc_start: 0.2046 (OUTLIER) cc_final: 0.1534 (m-10) REVERT: H 83 MET cc_start: -0.0835 (mtp) cc_final: -0.1288 (mmm) REVERT: H 114 MET cc_start: -0.1487 (mtm) cc_final: -0.1838 (mtp) REVERT: H 178 HIS cc_start: 0.0439 (OUTLIER) cc_final: -0.0000 (m-70) REVERT: I 34 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3243 (mpt) REVERT: I 83 MET cc_start: 0.2899 (mmp) cc_final: 0.1842 (mtp) REVERT: I 106 ASP cc_start: 0.4031 (OUTLIER) cc_final: 0.3625 (m-30) REVERT: I 114 MET cc_start: -0.0369 (OUTLIER) cc_final: -0.0697 (pp-130) REVERT: I 184 LEU cc_start: 0.2946 (OUTLIER) cc_final: 0.2369 (pt) REVERT: I 211 ASN cc_start: 0.1862 (OUTLIER) cc_final: 0.1523 (m110) outliers start: 164 outliers final: 87 residues processed: 276 average time/residue: 0.8461 time to fit residues: 305.4667 Evaluate side-chains 228 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 121 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 chunk 311 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 369 optimal weight: 40.0000 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN L 53 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31533 Z= 0.396 Angle : 0.731 10.909 42927 Z= 0.354 Chirality : 0.052 0.835 5077 Planarity : 0.005 0.052 5461 Dihedral : 7.969 100.688 5634 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.24 % Favored : 91.57 % Rotamer: Outliers : 5.34 % Allowed : 23.61 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3798 helix: 0.59 (0.20), residues: 709 sheet: -0.22 (0.15), residues: 1070 loop : -2.03 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 436 HIS 0.007 0.001 HIS B1048 PHE 0.027 0.002 PHE A 140 TYR 0.023 0.002 TYR B1067 ARG 0.007 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 128 time to evaluate : 3.286 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: A 333 THR cc_start: 0.5422 (OUTLIER) cc_final: 0.5108 (t) REVERT: A 379 CYS cc_start: 0.1346 (OUTLIER) cc_final: 0.0370 (p) REVERT: A 389 ASP cc_start: 0.4447 (OUTLIER) cc_final: 0.4141 (p0) REVERT: A 546 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6345 (mm) REVERT: A 855 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5791 (t80) REVERT: A 869 MET cc_start: 0.8856 (mtt) cc_final: 0.8582 (mtt) REVERT: A 1094 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8866 (t) REVERT: A 1113 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: B 153 MET cc_start: 0.3677 (OUTLIER) cc_final: 0.2186 (pp-130) REVERT: B 164 ASN cc_start: 0.3508 (OUTLIER) cc_final: 0.2530 (p0) REVERT: B 427 ASP cc_start: 0.1454 (OUTLIER) cc_final: 0.0878 (t70) REVERT: B 554 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6114 (tp30) REVERT: B 861 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9066 (mt) REVERT: B 900 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: B 933 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8190 (mtpt) REVERT: B 994 ASP cc_start: 0.7439 (t70) cc_final: 0.7212 (t0) REVERT: C 153 MET cc_start: 0.1924 (mpp) cc_final: 0.0278 (ttm) REVERT: C 233 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7018 (tp) REVERT: C 535 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7461 (ttmt) REVERT: H 60 TYR cc_start: 0.2067 (OUTLIER) cc_final: 0.1499 (m-10) REVERT: H 83 MET cc_start: -0.0330 (mtp) cc_final: -0.1109 (mmm) REVERT: H 114 MET cc_start: -0.1585 (mtm) cc_final: -0.1873 (mtp) REVERT: H 115 ASP cc_start: 0.2440 (OUTLIER) cc_final: 0.1065 (t0) REVERT: H 178 HIS cc_start: 0.0476 (OUTLIER) cc_final: 0.0003 (m-70) REVERT: I 34 MET cc_start: 0.4616 (OUTLIER) cc_final: 0.3398 (mpt) REVERT: I 83 MET cc_start: 0.2608 (mmp) cc_final: 0.1885 (mtp) REVERT: I 106 ASP cc_start: 0.3968 (OUTLIER) cc_final: 0.3560 (m-30) REVERT: I 184 LEU cc_start: 0.3072 (OUTLIER) cc_final: 0.2428 (pt) REVERT: I 211 ASN cc_start: 0.1928 (OUTLIER) cc_final: 0.1606 (m110) REVERT: M 192 ARG cc_start: 0.2055 (OUTLIER) cc_final: 0.1754 (tpt90) outliers start: 179 outliers final: 108 residues processed: 285 average time/residue: 0.8445 time to fit residues: 316.3991 Evaluate side-chains 249 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 117 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 220 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 487 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31533 Z= 0.240 Angle : 0.668 10.583 42927 Z= 0.322 Chirality : 0.048 0.742 5077 Planarity : 0.005 0.052 5461 Dihedral : 7.747 101.578 5634 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.50 % Favored : 92.31 % Rotamer: Outliers : 4.50 % Allowed : 24.53 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3798 helix: 0.80 (0.20), residues: 709 sheet: -0.07 (0.15), residues: 1061 loop : -1.92 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.006 0.001 HIS A 207 PHE 0.019 0.001 PHE A 201 TYR 0.019 0.001 TYR B1067 ARG 0.006 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 128 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.5182 (OUTLIER) cc_final: 0.4899 (t) REVERT: A 379 CYS cc_start: 0.1326 (OUTLIER) cc_final: 0.0359 (p) REVERT: A 389 ASP cc_start: 0.4402 (OUTLIER) cc_final: 0.4114 (p0) REVERT: A 546 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6398 (mm) REVERT: A 855 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5784 (t80) REVERT: A 1094 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8855 (t) REVERT: A 1113 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: A 1142 GLN cc_start: 0.7382 (tp40) cc_final: 0.7126 (tp40) REVERT: B 153 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.2154 (pp-130) REVERT: B 164 ASN cc_start: 0.3635 (OUTLIER) cc_final: 0.2638 (p0) REVERT: B 554 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6084 (tp30) REVERT: B 994 ASP cc_start: 0.7357 (t70) cc_final: 0.7143 (t0) REVERT: C 153 MET cc_start: 0.2109 (mpp) cc_final: 0.0380 (ttm) REVERT: C 233 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6882 (tp) REVERT: H 83 MET cc_start: -0.0141 (mtp) cc_final: -0.0936 (mmm) REVERT: H 114 MET cc_start: -0.1497 (mtm) cc_final: -0.1861 (mtp) REVERT: H 115 ASP cc_start: 0.2471 (OUTLIER) cc_final: 0.1076 (t0) REVERT: H 178 HIS cc_start: 0.0385 (OUTLIER) cc_final: -0.0061 (m-70) REVERT: I 34 MET cc_start: 0.4631 (OUTLIER) cc_final: 0.3530 (mpt) REVERT: I 83 MET cc_start: 0.2524 (mmp) cc_final: 0.1792 (mtp) REVERT: I 184 LEU cc_start: 0.2976 (OUTLIER) cc_final: 0.2327 (pt) REVERT: I 211 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.1619 (m110) outliers start: 151 outliers final: 98 residues processed: 260 average time/residue: 0.8876 time to fit residues: 310.6016 Evaluate side-chains 233 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 119 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 50.0000 chunk 353 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 325 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 31533 Z= 0.485 Angle : 0.784 11.947 42927 Z= 0.381 Chirality : 0.054 0.869 5077 Planarity : 0.005 0.059 5461 Dihedral : 8.156 104.033 5631 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.84 % Rotamer: Outliers : 4.50 % Allowed : 24.62 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3798 helix: 0.43 (0.20), residues: 709 sheet: -0.16 (0.15), residues: 1083 loop : -2.07 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 98 HIS 0.009 0.002 HIS B1048 PHE 0.025 0.003 PHE A 140 TYR 0.023 0.002 TYR B1067 ARG 0.009 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 127 time to evaluate : 3.387 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: A 333 THR cc_start: 0.5362 (OUTLIER) cc_final: 0.5097 (t) REVERT: A 379 CYS cc_start: 0.1342 (OUTLIER) cc_final: 0.0509 (p) REVERT: A 389 ASP cc_start: 0.4887 (OUTLIER) cc_final: 0.4612 (p0) REVERT: A 546 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6431 (mm) REVERT: A 1113 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: A 1142 GLN cc_start: 0.7497 (tp40) cc_final: 0.7175 (tp40) REVERT: B 153 MET cc_start: 0.3799 (OUTLIER) cc_final: 0.2248 (pp-130) REVERT: B 164 ASN cc_start: 0.3327 (OUTLIER) cc_final: 0.2367 (p0) REVERT: B 233 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5932 (tp) REVERT: B 455 LEU cc_start: 0.2313 (OUTLIER) cc_final: 0.1853 (tp) REVERT: B 554 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6130 (tp30) REVERT: B 933 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8164 (mtpt) REVERT: B 994 ASP cc_start: 0.7578 (t70) cc_final: 0.7355 (t0) REVERT: C 153 MET cc_start: 0.2115 (mpp) cc_final: 0.1046 (ttt) REVERT: C 233 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7077 (tp) REVERT: C 535 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7489 (ttmt) REVERT: H 83 MET cc_start: -0.0124 (mtp) cc_final: -0.0644 (mmm) REVERT: H 115 ASP cc_start: 0.2749 (OUTLIER) cc_final: 0.0933 (t0) REVERT: H 178 HIS cc_start: 0.0573 (OUTLIER) cc_final: 0.0085 (m-70) REVERT: I 34 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.3490 (mpt) REVERT: I 83 MET cc_start: 0.2381 (mmp) cc_final: 0.1586 (mtp) REVERT: M 192 ARG cc_start: 0.2002 (OUTLIER) cc_final: 0.1717 (tpt90) outliers start: 151 outliers final: 95 residues processed: 256 average time/residue: 0.8426 time to fit residues: 281.6513 Evaluate side-chains 229 residues out of total 3355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 117 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 192 ARG Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 50.4742 > 50: distance: 79 - 86: 19.276 distance: 80 - 99: 9.476 distance: 86 - 87: 22.662 distance: 87 - 88: 6.017 distance: 87 - 90: 6.120 distance: 88 - 89: 20.364 distance: 88 - 94: 7.611 distance: 89 - 107: 21.156 distance: 90 - 91: 14.910 distance: 90 - 92: 25.516 distance: 91 - 93: 21.057 distance: 94 - 95: 23.115 distance: 95 - 96: 28.660 distance: 95 - 98: 28.358 distance: 96 - 97: 28.909 distance: 96 - 99: 8.116 distance: 99 - 100: 15.145 distance: 100 - 101: 25.499 distance: 100 - 103: 14.699 distance: 101 - 102: 23.230 distance: 101 - 107: 25.869 distance: 103 - 104: 13.164 distance: 104 - 105: 35.663 distance: 104 - 106: 33.685 distance: 107 - 108: 10.065 distance: 108 - 109: 6.357 distance: 108 - 111: 6.333 distance: 109 - 110: 3.865 distance: 109 - 119: 3.423 distance: 116 - 117: 3.336 distance: 119 - 120: 9.947 distance: 120 - 121: 14.189 distance: 120 - 123: 5.216 distance: 121 - 127: 8.416 distance: 123 - 124: 9.858 distance: 124 - 125: 9.600 distance: 124 - 126: 4.856 distance: 128 - 129: 17.752 distance: 128 - 131: 6.124 distance: 129 - 130: 11.885 distance: 129 - 139: 25.068 distance: 131 - 132: 8.544 distance: 132 - 133: 5.772 distance: 132 - 134: 5.223 distance: 133 - 135: 9.911 distance: 134 - 136: 11.897 distance: 135 - 137: 6.283 distance: 136 - 137: 6.292 distance: 137 - 138: 3.154 distance: 139 - 140: 10.484 distance: 140 - 141: 38.800 distance: 140 - 143: 13.537 distance: 141 - 142: 35.149 distance: 141 - 148: 7.080 distance: 143 - 144: 25.661 distance: 144 - 145: 18.390 distance: 145 - 146: 26.644 distance: 146 - 147: 30.274 distance: 148 - 149: 9.515 distance: 149 - 150: 37.846 distance: 149 - 152: 30.580 distance: 150 - 151: 16.103 distance: 150 - 156: 26.829 distance: 152 - 153: 20.789 distance: 153 - 154: 20.481 distance: 153 - 155: 23.021 distance: 156 - 157: 23.237 distance: 156 - 162: 19.707 distance: 157 - 158: 10.681 distance: 157 - 160: 37.975 distance: 158 - 159: 16.188 distance: 158 - 163: 12.374 distance: 160 - 161: 15.732 distance: 161 - 162: 16.897 distance: 163 - 164: 17.218 distance: 164 - 165: 22.451 distance: 164 - 167: 11.970 distance: 165 - 166: 17.311 distance: 165 - 171: 11.124 distance: 167 - 168: 19.702 distance: 168 - 169: 23.283 distance: 168 - 170: 20.167