Starting phenix.real_space_refine on Thu Jul 25 00:04:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybm_33726/07_2024/7ybm_33726.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybm_33726/07_2024/7ybm_33726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybm_33726/07_2024/7ybm_33726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybm_33726/07_2024/7ybm_33726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybm_33726/07_2024/7ybm_33726.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybm_33726/07_2024/7ybm_33726.cif" } resolution = 3.45 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 114 5.16 5 C 17439 2.51 5 N 4416 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27456 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8645 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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: "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: 14.11, per 1000 atoms: 0.51 Number of scatterers: 27456 At special positions: 0 Unit cell: (142.31, 150.87, 196.88, 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 114 16.00 O 5487 8.00 N 4416 7.00 C 17439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 343 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG A1408 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 343 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 657 " " NAG B1407 " - " ASN B 709 " " NAG B1408 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 4.4 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6198 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 47 sheets defined 26.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.190A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.755A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.925A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.541A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.909A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.730A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.577A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.860A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.600A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 939 removed outlier: 3.703A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.544A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.720A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.715A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.871A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.754A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.321A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.739A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.534A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.704A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.806A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.648A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.092A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 3.910A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.631A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.608A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.789A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.074A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.771A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.805A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.677A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.683A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 939 removed outlier: 3.668A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.917A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.328A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.319A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 94 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 43 current: chain 'B' and resid 538 through 543 removed outlier: 3.549A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 546 through 547 current: chain 'B' and resid 573 through 577 removed outlier: 5.333A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 54 removed outlier: 7.559A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.506A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.147A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.887A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.295A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.852A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.798A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 718 through 728 current: chain 'A' and resid 1059 through 1069 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.395A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.551A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 64 current: chain 'B' and resid 187 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 187 through 189 current: chain 'B' and resid 200 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.504A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.975A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.570A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.529A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.607A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.554A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 718 through 728 current: chain 'B' and resid 1059 through 1069 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.534A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.251A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.543A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.559A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.297A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.937A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.772A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.601A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1076 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.597A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 910 hydrogen bonds defined for protein. 2493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.55 Time building geometry restraints manager: 12.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8549 1.34 - 1.46: 7183 1.46 - 1.59: 12181 1.59 - 1.71: 2 1.71 - 1.83: 144 Bond restraints: 28059 Sorted by residual: bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.12e-02 7.97e+03 1.36e+01 bond pdb=" CB PRO B 589 " pdb=" CG PRO B 589 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.74e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C5 MAN U 3 " pdb=" O5 MAN U 3 " ideal model delta sigma weight residual 1.418 1.464 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" C5 MAN J 3 " pdb=" O5 MAN J 3 " ideal model delta sigma weight residual 1.418 1.463 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 28054 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.93: 619 105.93 - 113.04: 15533 113.04 - 120.16: 9589 120.16 - 127.27: 12184 127.27 - 134.39: 226 Bond angle restraints: 38151 Sorted by residual: angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.46e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.31 110.41 -7.10 8.90e-01 1.26e+00 6.37e+01 angle pdb=" CA PRO B 589 " pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 112.00 100.92 11.08 1.40e+00 5.10e-01 6.27e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.27 110.23 -6.96 9.00e-01 1.23e+00 5.98e+01 angle pdb=" N PRO B 899 " pdb=" CA PRO B 899 " pdb=" CB PRO B 899 " ideal model delta sigma weight residual 103.51 110.05 -6.54 9.60e-01 1.09e+00 4.65e+01 ... (remaining 38146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 17098 25.06 - 50.11: 832 50.11 - 75.17: 110 75.17 - 100.23: 73 100.23 - 125.29: 37 Dihedral angle restraints: 18150 sinusoidal: 8517 harmonic: 9633 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -171.05 85.05 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -167.39 81.39 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -159.80 73.80 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 18147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 4624 0.240 - 0.479: 11 0.479 - 0.719: 0 0.719 - 0.959: 1 0.959 - 1.198: 1 Chirality restraints: 4637 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.20 -1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 4634 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 588 " 0.094 5.00e-02 4.00e+02 1.34e-01 2.89e+01 pdb=" N PRO B 589 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " -0.004 2.00e-02 2.50e+03 3.86e-02 1.87e+01 pdb=" CG ASN B 717 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.069 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 589 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.055 5.00e-02 4.00e+02 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 416 2.65 - 3.22: 25520 3.22 - 3.78: 40434 3.78 - 4.34: 55053 4.34 - 4.90: 90004 Nonbonded interactions: 211427 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.092 2.440 nonbonded pdb=" OE2 GLU B 988 " pdb=" OG SER C 383 " model vdw 2.159 2.440 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.164 2.440 nonbonded pdb=" O ALA B 924 " pdb=" ND2 ASN B 928 " model vdw 2.170 2.520 nonbonded pdb=" OG SER A 383 " pdb=" OE2 GLU C 988 " model vdw 2.170 2.440 ... (remaining 211422 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 71.180 Find NCS groups from input model: 4.900 Set up NCS constraints: 0.130 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.004 0.148 28059 Z= 0.279 Angle : 0.770 11.812 38151 Z= 0.421 Chirality : 0.052 1.198 4637 Planarity : 0.005 0.134 4770 Dihedral : 16.149 125.287 11835 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.07 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3267 helix: 1.63 (0.20), residues: 747 sheet: -0.37 (0.22), residues: 555 loop : -1.28 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 633 HIS 0.021 0.001 HIS A 66 PHE 0.024 0.001 PHE C 275 TYR 0.017 0.001 TYR B1138 ARG 0.007 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.5873 (t) cc_final: 0.5555 (t) REVERT: C 735 SER cc_start: 0.7570 (t) cc_final: 0.7368 (t) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.3412 time to fit residues: 127.8586 Evaluate side-chains 158 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.6980 chunk 250 optimal weight: 10.0000 chunk 138 optimal weight: 0.0000 chunk 85 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 317 ASN A 394 ASN A 437 ASN A 965 GLN B 66 HIS B 317 ASN B 542 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28059 Z= 0.231 Angle : 0.667 13.521 38151 Z= 0.321 Chirality : 0.046 0.558 4637 Planarity : 0.004 0.073 4770 Dihedral : 13.200 105.351 5883 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 0.80 % Allowed : 5.30 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3267 helix: 1.71 (0.20), residues: 741 sheet: -0.44 (0.21), residues: 609 loop : -1.40 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.005 0.001 HIS A 66 PHE 0.021 0.002 PHE B 643 TYR 0.023 0.002 TYR A 266 ARG 0.007 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.5864 (t) cc_final: 0.5406 (t) REVERT: B 509 ARG cc_start: 0.3887 (ttm170) cc_final: 0.3477 (ttp-170) REVERT: C 59 PHE cc_start: 0.4786 (OUTLIER) cc_final: 0.3801 (t80) outliers start: 23 outliers final: 18 residues processed: 195 average time/residue: 0.3620 time to fit residues: 116.9983 Evaluate side-chains 166 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 0.0050 chunk 93 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 267 optimal weight: 20.0000 chunk 297 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 437 ASN A 965 GLN B 66 HIS B 146 HIS B 580 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28059 Z= 0.185 Angle : 0.638 12.834 38151 Z= 0.301 Chirality : 0.045 0.525 4637 Planarity : 0.004 0.058 4770 Dihedral : 12.156 102.722 5883 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 1.28 % Allowed : 8.52 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3267 helix: 1.81 (0.20), residues: 741 sheet: -0.37 (0.21), residues: 606 loop : -1.38 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.004 0.001 HIS C1058 PHE 0.022 0.001 PHE A 318 TYR 0.017 0.001 TYR B1138 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 CYS cc_start: 0.5707 (t) cc_final: 0.5455 (t) REVERT: A 878 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7482 (tt) REVERT: B 509 ARG cc_start: 0.4081 (ttm170) cc_final: 0.3796 (ttp-170) REVERT: C 542 ASN cc_start: 0.8137 (p0) cc_final: 0.7815 (p0) REVERT: C 878 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8067 (tt) outliers start: 37 outliers final: 25 residues processed: 193 average time/residue: 0.3670 time to fit residues: 119.7784 Evaluate side-chains 174 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 146 HIS B 185 ASN B 542 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28059 Z= 0.275 Angle : 0.690 13.210 38151 Z= 0.326 Chirality : 0.046 0.519 4637 Planarity : 0.004 0.050 4770 Dihedral : 10.564 92.878 5883 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.49 % Favored : 93.42 % Rotamer: Outliers : 1.90 % Allowed : 9.87 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3267 helix: 1.63 (0.20), residues: 744 sheet: -0.47 (0.20), residues: 651 loop : -1.49 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.023 0.001 HIS B 66 PHE 0.022 0.002 PHE B 65 TYR 0.019 0.002 TYR B1067 ARG 0.004 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 160 time to evaluate : 2.802 Fit side-chains revert: symmetry clash REVERT: A 529 LYS cc_start: 0.5499 (OUTLIER) cc_final: 0.5224 (ptmm) REVERT: A 738 CYS cc_start: 0.5621 (t) cc_final: 0.5394 (t) REVERT: A 878 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7594 (tt) REVERT: A 902 MET cc_start: 0.8539 (mmt) cc_final: 0.8224 (mmt) REVERT: A 957 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7852 (tm-30) REVERT: B 509 ARG cc_start: 0.4040 (ttm170) cc_final: 0.3699 (ttp-170) REVERT: C 878 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8094 (tt) REVERT: C 904 TYR cc_start: 0.7525 (m-10) cc_final: 0.7296 (m-10) outliers start: 55 outliers final: 29 residues processed: 206 average time/residue: 0.3498 time to fit residues: 122.5914 Evaluate side-chains 178 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 162 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 437 ASN A1011 GLN A1142 GLN B 66 HIS B 115 GLN B 146 HIS B 542 ASN ** B1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 207 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 644 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 28059 Z= 0.533 Angle : 0.917 13.988 38151 Z= 0.448 Chirality : 0.055 0.523 4637 Planarity : 0.006 0.057 4770 Dihedral : 9.760 76.708 5883 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 2.56 % Allowed : 12.43 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3267 helix: 0.95 (0.19), residues: 726 sheet: -0.72 (0.20), residues: 672 loop : -1.94 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 886 HIS 0.025 0.003 HIS B 66 PHE 0.031 0.003 PHE B 201 TYR 0.034 0.003 TYR B1067 ARG 0.007 0.001 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 175 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8022 (tt) REVERT: B 395 VAL cc_start: 0.7802 (t) cc_final: 0.7476 (t) REVERT: C 321 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: C 850 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 878 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8320 (tt) outliers start: 74 outliers final: 46 residues processed: 244 average time/residue: 0.3569 time to fit residues: 145.1701 Evaluate side-chains 193 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 143 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.0470 chunk 287 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 chunk 265 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN B 146 HIS B 779 GLN B1135 ASN C 81 ASN C 542 ASN C 658 ASN C1002 GLN C1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28059 Z= 0.222 Angle : 0.701 14.817 38151 Z= 0.330 Chirality : 0.046 0.516 4637 Planarity : 0.004 0.052 4770 Dihedral : 8.709 82.503 5883 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 2.04 % Allowed : 13.78 % Favored : 84.18 % 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: -1.08 (0.14), residues: 3267 helix: 1.60 (0.20), residues: 717 sheet: -0.72 (0.20), residues: 639 loop : -1.71 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.006 0.001 HIS A 519 PHE 0.029 0.002 PHE C 192 TYR 0.021 0.001 TYR A 266 ARG 0.009 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.1589 (OUTLIER) cc_final: 0.0762 (m-40) REVERT: A 735 SER cc_start: 0.8068 (t) cc_final: 0.7772 (p) REVERT: A 878 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7535 (tt) REVERT: C 48 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8474 (mp) REVERT: C 740 MET cc_start: 0.7155 (ttm) cc_final: 0.6813 (ttm) REVERT: C 878 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8135 (tt) outliers start: 59 outliers final: 31 residues processed: 219 average time/residue: 0.3547 time to fit residues: 131.1426 Evaluate side-chains 180 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS B 542 ASN C 542 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28059 Z= 0.281 Angle : 0.714 15.196 38151 Z= 0.336 Chirality : 0.047 0.515 4637 Planarity : 0.004 0.047 4770 Dihedral : 8.345 83.454 5883 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 2.08 % Allowed : 14.26 % Favored : 83.66 % 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: -1.08 (0.14), residues: 3267 helix: 1.57 (0.19), residues: 729 sheet: -0.64 (0.20), residues: 618 loop : -1.74 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 353 HIS 0.006 0.001 HIS A1058 PHE 0.031 0.002 PHE A 92 TYR 0.019 0.002 TYR C 170 ARG 0.006 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 149 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 878 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7666 (tt) REVERT: A 977 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 542 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7612 (p0) REVERT: C 850 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 878 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8165 (tt) outliers start: 60 outliers final: 43 residues processed: 202 average time/residue: 0.3588 time to fit residues: 123.4357 Evaluate side-chains 190 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 142 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1135 ASN B 542 ASN B 779 GLN C 542 ASN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28059 Z= 0.243 Angle : 0.682 15.560 38151 Z= 0.321 Chirality : 0.046 0.551 4637 Planarity : 0.004 0.045 4770 Dihedral : 8.008 83.808 5883 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer: Outliers : 2.28 % Allowed : 14.61 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3267 helix: 1.66 (0.20), residues: 729 sheet: -0.66 (0.20), residues: 639 loop : -1.65 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.006 0.001 HIS A 519 PHE 0.022 0.002 PHE B 543 TYR 0.017 0.001 TYR A 265 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 157 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.1160 (OUTLIER) cc_final: 0.0584 (m-40) REVERT: A 88 ASP cc_start: 0.4893 (OUTLIER) cc_final: 0.4581 (p0) REVERT: A 878 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 977 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8389 (mp) REVERT: C 48 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (mp) REVERT: C 850 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8069 (mp) REVERT: C 878 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8082 (tt) outliers start: 66 outliers final: 43 residues processed: 215 average time/residue: 0.3394 time to fit residues: 124.8488 Evaluate side-chains 199 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 278 optimal weight: 0.5980 chunk 296 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 232 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 295 optimal weight: 0.7980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 437 ASN A1106 GLN B 542 ASN C 81 ASN C 207 HIS ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28059 Z= 0.173 Angle : 0.649 15.464 38151 Z= 0.303 Chirality : 0.045 0.511 4637 Planarity : 0.004 0.046 4770 Dihedral : 7.620 84.341 5883 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 1.77 % Allowed : 15.09 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3267 helix: 1.89 (0.20), residues: 723 sheet: -0.55 (0.20), residues: 639 loop : -1.56 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 353 HIS 0.005 0.001 HIS A 519 PHE 0.019 0.001 PHE C 192 TYR 0.020 0.001 TYR B 396 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.1138 (OUTLIER) cc_final: 0.0525 (m-40) REVERT: A 88 ASP cc_start: 0.4940 (OUTLIER) cc_final: 0.4635 (p0) REVERT: A 878 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7418 (tt) REVERT: C 48 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 542 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7694 (p0) REVERT: C 878 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8138 (tt) outliers start: 51 outliers final: 39 residues processed: 211 average time/residue: 0.3376 time to fit residues: 121.3897 Evaluate side-chains 198 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 153 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 542 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 261 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 542 ASN C 81 ASN C 207 HIS C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28059 Z= 0.259 Angle : 0.683 15.635 38151 Z= 0.321 Chirality : 0.046 0.512 4637 Planarity : 0.004 0.047 4770 Dihedral : 7.547 82.427 5883 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 1.83 % Allowed : 15.30 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3267 helix: 1.80 (0.20), residues: 723 sheet: -0.60 (0.19), residues: 738 loop : -1.55 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.005 0.001 HIS A 519 PHE 0.020 0.002 PHE C 192 TYR 0.023 0.001 TYR B 396 ARG 0.005 0.000 ARG B 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 151 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.1103 (OUTLIER) cc_final: 0.0384 (m-40) REVERT: A 88 ASP cc_start: 0.5039 (OUTLIER) cc_final: 0.4675 (p0) REVERT: A 878 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7593 (tt) REVERT: A 957 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7864 (tm-30) REVERT: C 48 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 214 ARG cc_start: 0.4029 (mmm160) cc_final: 0.3433 (ttm170) REVERT: C 277 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6032 (mt) REVERT: C 850 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8052 (mp) REVERT: C 878 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8057 (tt) outliers start: 53 outliers final: 40 residues processed: 196 average time/residue: 0.3405 time to fit residues: 114.0987 Evaluate side-chains 195 residues out of total 2898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 0.0770 chunk 80 optimal weight: 0.0060 chunk 241 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1106 GLN B 542 ASN C 81 ASN C 207 HIS C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.203521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.168773 restraints weight = 44309.243| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.76 r_work: 0.3868 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28059 Z= 0.157 Angle : 0.638 14.924 38151 Z= 0.298 Chirality : 0.045 0.510 4637 Planarity : 0.004 0.046 4770 Dihedral : 7.112 81.472 5883 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 1.56 % Allowed : 15.37 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3267 helix: 2.02 (0.20), residues: 729 sheet: -0.46 (0.20), residues: 639 loop : -1.46 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.004 0.001 HIS A 519 PHE 0.017 0.001 PHE C 192 TYR 0.022 0.001 TYR B 396 ARG 0.005 0.000 ARG B 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4709.44 seconds wall clock time: 87 minutes 32.27 seconds (5252.27 seconds total)