Starting phenix.real_space_refine on Wed Mar 20 19:31:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2d_23125/03_2024/7l2d_23125.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2d_23125/03_2024/7l2d_23125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2d_23125/03_2024/7l2d_23125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2d_23125/03_2024/7l2d_23125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2d_23125/03_2024/7l2d_23125.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2d_23125/03_2024/7l2d_23125.pdb" } resolution = 3.55 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= 0.033 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 124 5.16 5 C 17985 2.51 5 N 4617 2.21 5 O 5602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28328 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1100, 8564 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 1100, 8564 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 8737 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 971 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 799 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 8449 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 bond proxies already assigned to first conformer: 8625 Chain: "C" Number of atoms: 8451 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1078, 8439 Classifications: {'peptide': 1078} Link IDs: {'PTRANS': 54, 'TRANS': 1023} Chain breaks: 5 bond proxies already assigned to first conformer: 8622 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ATYR A 365 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 365 " occ=0.50 residue: pdb=" N ATYR A 369 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 369 " occ=0.50 Time building chain proxies: 26.40, per 1000 atoms: 0.93 Number of scatterers: 28328 At special positions: 0 Unit cell: (143.38, 182.97, 185.11, 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 124 16.00 O 5602 8.00 N 4617 7.00 C 17985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.15 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " 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=2.05 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 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 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 S 2 " - " BMA S 3 " " 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 Y 2 " - " BMA Y 3 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 17 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 17 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 149 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 343 " " NAG B1311 " - " ASN B 603 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 149 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 17 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN A1134 " " NAG I 1 " - " ASN A 122 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 165 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 234 " Time building additional restraints: 11.77 Conformation dependent library (CDL) restraints added in 9.6 seconds 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 55 sheets defined 23.1% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.517A pdb=" N GLU A 180 " --> pdb=" O MET A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.716A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.564A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 5.796A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.818A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.204A pdb=" N THR A 887 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.423A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.694A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.394A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.785A pdb=" N ASP A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'L' and resid 27B through 30 removed outlier: 3.546A pdb=" N TYR L 30 " --> pdb=" O VAL L 27C" (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.553A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.868A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.733A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.353A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 5.806A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.924A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 4.011A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.524A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.553A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.596A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.088A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.015A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.171A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 568 through 572 removed outlier: 4.108A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.941A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 783 removed outlier: 5.815A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.696A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.501A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.161A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.838A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.615A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.317A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.307A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.307A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.097A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.954A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.173A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 68 through 71 removed outlier: 6.236A pdb=" N HIS A 69 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 77 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 75 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.524A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.499A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.667A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.882A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.448A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.928A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.492A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.888A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.869A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.527A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.681A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET H 80 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 39 Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.538A pdb=" N VAL L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AC7, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.523A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.019A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.418A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.815A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.498A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.168A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.979A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.108A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.106A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.908A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.782A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1098 Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.004A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.545A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.750A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.557A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.016A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.453A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.191A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.654A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.101A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.787A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1094 through 1097 1069 hydrogen bonds defined for protein. 2895 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: 12.37 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4564 1.32 - 1.44: 8252 1.44 - 1.57: 15998 1.57 - 1.70: 1 1.70 - 1.82: 160 Bond restraints: 28975 Sorted by residual: bond pdb=" C TYR C 365 " pdb=" O TYR C 365 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.29e-02 6.01e+03 9.60e+01 bond pdb=" C TYR B 365 " pdb=" O TYR B 365 " ideal model delta sigma weight residual 1.236 1.358 -0.122 1.29e-02 6.01e+03 8.97e+01 bond pdb=" C PRO B 792 " pdb=" N PRO B 793 " ideal model delta sigma weight residual 1.328 1.382 -0.054 1.25e-02 6.40e+03 1.85e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.57e+01 ... (remaining 28970 not shown) Histogram of bond angle deviations from ideal: 93.25 - 101.48: 39 101.48 - 109.72: 4106 109.72 - 117.95: 18256 117.95 - 126.18: 16699 126.18 - 134.41: 358 Bond angle restraints: 39458 Sorted by residual: angle pdb=" O TYR B 365 " pdb=" C TYR B 365 " pdb=" CA BTYR B 365 " ideal model delta sigma weight residual 119.38 133.13 -13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" O TYR C 365 " pdb=" C TYR C 365 " pdb=" CA BTYR C 365 " ideal model delta sigma weight residual 119.38 132.63 -13.25 1.23e+00 6.61e-01 1.16e+02 angle pdb=" O TYR B 365 " pdb=" C TYR B 365 " pdb=" CA ATYR B 365 " ideal model delta sigma weight residual 119.05 132.75 -13.70 1.30e+00 5.92e-01 1.11e+02 angle pdb=" O TYR C 365 " pdb=" C TYR C 365 " pdb=" CA ATYR C 365 " ideal model delta sigma weight residual 119.05 132.45 -13.40 1.30e+00 5.92e-01 1.06e+02 angle pdb=" N GLN A 218 " pdb=" CA GLN A 218 " pdb=" C GLN A 218 " ideal model delta sigma weight residual 113.19 104.21 8.98 1.19e+00 7.06e-01 5.69e+01 ... (remaining 39453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 17163 21.50 - 43.00: 891 43.00 - 64.49: 120 64.49 - 85.99: 47 85.99 - 107.49: 14 Dihedral angle restraints: 18235 sinusoidal: 8053 harmonic: 10182 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -173.34 87.34 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 169.05 -76.05 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 159.59 -66.59 1 1.00e+01 1.00e-02 5.79e+01 ... (remaining 18232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 4656 0.284 - 0.568: 22 0.568 - 0.852: 2 0.852 - 1.136: 2 1.136 - 1.420: 3 Chirality restraints: 4685 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.06e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.06e+02 ... (remaining 4682 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.357 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG F 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.351 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1304 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.095 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG B1311 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.149 2.00e-02 2.50e+03 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5694 2.78 - 3.31: 25590 3.31 - 3.84: 46610 3.84 - 4.37: 54075 4.37 - 4.90: 93056 Nonbonded interactions: 225025 Sorted by model distance: nonbonded pdb=" OG1 THR A 553 " pdb=" OD1 ASP A 586 " model vdw 2.252 2.440 nonbonded pdb=" OG SER A 884 " pdb=" OG1 THR A 887 " model vdw 2.266 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.276 2.440 nonbonded pdb=" OG SER C 673 " pdb=" OH TYR C 695 " model vdw 2.279 2.440 nonbonded pdb=" O ASP C 994 " pdb=" OG1 THR C 998 " model vdw 2.281 2.440 ... (remaining 225020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 69 or resid 77 through 179 or resid 184 through \ 246 or resid 257 through 364 or resid 366 through 368 or resid 370 through 476 \ or resid 478 through 829 or resid 853 through 1147 or resid 1301 through 1311)) selection = (chain 'B' and (resid 14 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 or (resid 185 through 186 and (name N o \ r name CA or name C or name O or name CB )) or resid 187 through 364 or resid 36 \ 6 through 368 or resid 370 through 476 or resid 478 through 1147 or resid 1301 t \ hrough 1311)) selection = (chain 'C' and (resid 14 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 or (resid 185 through 186 and (name N o \ r name CA or name C or name O or name CB )) or resid 187 through 364 or resid 36 \ 6 through 368 or resid 370 through 476 or resid 478 through 1147 or resid 1301 t \ hrough 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.800 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 94.700 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.370 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 28975 Z= 0.415 Angle : 1.033 13.749 39458 Z= 0.659 Chirality : 0.082 1.420 4685 Planarity : 0.017 0.305 5003 Dihedral : 13.258 107.491 11569 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.33 % Allowed : 2.01 % Favored : 97.66 % Cbeta Deviations : 0.15 % 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: -0.67 (0.13), residues: 3467 helix: -0.11 (0.18), residues: 701 sheet: 0.37 (0.18), residues: 766 loop : -0.88 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 103 HIS 0.024 0.001 HIS B1048 PHE 0.036 0.002 PHE B1121 TYR 0.027 0.002 TYR C 904 ARG 0.031 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 355 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8993 (m) cc_final: 0.8504 (p) REVERT: A 919 ASN cc_start: 0.8267 (m-40) cc_final: 0.7900 (t0) REVERT: H 72 ASP cc_start: 0.8032 (t70) cc_final: 0.7745 (t0) REVERT: H 85 GLU cc_start: 0.6012 (tp30) cc_final: 0.5600 (pm20) REVERT: H 100 MET cc_start: 0.5079 (pmm) cc_final: 0.4350 (ptp) REVERT: L 5 THR cc_start: 0.7765 (p) cc_final: 0.7562 (t) REVERT: L 95 THR cc_start: 0.4333 (m) cc_final: 0.3910 (p) REVERT: B 389 ASP cc_start: 0.7949 (t0) cc_final: 0.7411 (t0) REVERT: B 571 ASP cc_start: 0.7300 (p0) cc_final: 0.6909 (p0) REVERT: B 886 TRP cc_start: 0.7313 (p90) cc_final: 0.7043 (p90) REVERT: B 934 ILE cc_start: 0.8997 (mm) cc_final: 0.8719 (mm) REVERT: C 139 PRO cc_start: 0.8731 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: C 313 TYR cc_start: 0.8645 (m-80) cc_final: 0.8191 (m-80) REVERT: C 558 LYS cc_start: 0.7411 (mttt) cc_final: 0.7199 (tppt) REVERT: C 776 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8774 (ttpp) outliers start: 9 outliers final: 1 residues processed: 362 average time/residue: 0.3553 time to fit residues: 214.2564 Evaluate side-chains 210 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 134 GLN A 207 HIS A 856 ASN A 901 GLN L 1 GLN B 388 ASN B 580 GLN B 764 ASN B 856 ASN B 919 ASN B1005 GLN B1101 HIS C 14 GLN C 787 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 28975 Z= 0.385 Angle : 0.719 12.000 39458 Z= 0.362 Chirality : 0.048 0.318 4685 Planarity : 0.005 0.070 5003 Dihedral : 7.782 65.357 5377 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.45 % Allowed : 7.93 % Favored : 90.62 % 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: -0.41 (0.13), residues: 3467 helix: 0.55 (0.19), residues: 735 sheet: 0.20 (0.18), residues: 789 loop : -0.78 (0.13), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 152 HIS 0.009 0.002 HIS A 207 PHE 0.037 0.002 PHE B 55 TYR 0.032 0.002 TYR C 369 ARG 0.011 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8409 (mtt) cc_final: 0.8116 (mtp) REVERT: H 85 GLU cc_start: 0.5607 (tp30) cc_final: 0.5376 (pm20) REVERT: H 100 TYR cc_start: 0.8368 (t80) cc_final: 0.8163 (t80) REVERT: H 100 TYR cc_start: 0.6734 (m-80) cc_final: 0.5723 (m-80) REVERT: B 707 TYR cc_start: 0.7203 (t80) cc_final: 0.6487 (t80) REVERT: B 886 TRP cc_start: 0.7510 (p90) cc_final: 0.6964 (p90) REVERT: C 558 LYS cc_start: 0.7470 (mttt) cc_final: 0.7236 (tppt) outliers start: 43 outliers final: 31 residues processed: 237 average time/residue: 0.3645 time to fit residues: 144.3576 Evaluate side-chains 205 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 314 optimal weight: 5.9990 chunk 340 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A 856 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 804 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28975 Z= 0.258 Angle : 0.596 10.439 39458 Z= 0.306 Chirality : 0.045 0.273 4685 Planarity : 0.004 0.060 5003 Dihedral : 6.832 59.844 5377 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.45 % Allowed : 9.51 % Favored : 89.05 % 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: -0.25 (0.14), residues: 3467 helix: 0.86 (0.19), residues: 735 sheet: 0.25 (0.18), residues: 766 loop : -0.72 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 152 HIS 0.005 0.001 HIS B1048 PHE 0.025 0.002 PHE B 55 TYR 0.022 0.001 TYR B1067 ARG 0.005 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 2.899 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 900 MET cc_start: 0.8407 (mtt) cc_final: 0.8084 (mtp) REVERT: H 59 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5687 (m-80) REVERT: H 100 TYR cc_start: 0.8365 (t80) cc_final: 0.7983 (t80) REVERT: H 100 TYR cc_start: 0.6897 (m-80) cc_final: 0.6144 (m-80) REVERT: H 100 MET cc_start: 0.6191 (pmm) cc_final: 0.5495 (ptp) REVERT: H 103 TRP cc_start: 0.8339 (m-10) cc_final: 0.8053 (m-10) REVERT: B 707 TYR cc_start: 0.7247 (t80) cc_final: 0.6657 (t80) REVERT: B 886 TRP cc_start: 0.7535 (p90) cc_final: 0.7006 (p90) REVERT: C 558 LYS cc_start: 0.7445 (mttt) cc_final: 0.7181 (tppt) outliers start: 43 outliers final: 29 residues processed: 221 average time/residue: 0.3436 time to fit residues: 129.9853 Evaluate side-chains 203 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 211 optimal weight: 0.7980 chunk 315 optimal weight: 7.9990 chunk 334 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 28975 Z= 0.361 Angle : 0.643 11.126 39458 Z= 0.329 Chirality : 0.045 0.254 4685 Planarity : 0.004 0.054 5003 Dihedral : 6.568 59.003 5375 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.17 % Allowed : 10.33 % Favored : 87.50 % 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: -0.36 (0.14), residues: 3467 helix: 0.87 (0.19), residues: 730 sheet: -0.02 (0.18), residues: 786 loop : -0.74 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 152 HIS 0.006 0.001 HIS B 207 PHE 0.027 0.002 PHE B 55 TYR 0.029 0.002 TYR C 495 ARG 0.006 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 178 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8412 (m-80) cc_final: 0.7955 (m-10) REVERT: A 569 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8345 (mm) REVERT: A 900 MET cc_start: 0.8542 (mtt) cc_final: 0.8326 (mtp) REVERT: H 59 TYR cc_start: 0.5884 (OUTLIER) cc_final: 0.5645 (m-80) REVERT: H 100 TYR cc_start: 0.8300 (t80) cc_final: 0.8087 (t80) REVERT: H 100 TYR cc_start: 0.7018 (m-80) cc_final: 0.6142 (m-80) REVERT: H 103 TRP cc_start: 0.8372 (m-10) cc_final: 0.8036 (m-10) REVERT: B 707 TYR cc_start: 0.7405 (t80) cc_final: 0.6902 (t80) REVERT: B 886 TRP cc_start: 0.7570 (p90) cc_final: 0.7213 (p90) REVERT: C 369 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: C 558 LYS cc_start: 0.7556 (mttt) cc_final: 0.7219 (tppt) REVERT: C 902 MET cc_start: 0.9008 (tpp) cc_final: 0.8469 (tpp) outliers start: 65 outliers final: 45 residues processed: 224 average time/residue: 0.3581 time to fit residues: 136.3773 Evaluate side-chains 216 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 300 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28975 Z= 0.156 Angle : 0.545 9.341 39458 Z= 0.279 Chirality : 0.044 0.270 4685 Planarity : 0.004 0.054 5003 Dihedral : 5.916 54.335 5375 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.45 % Allowed : 11.55 % Favored : 87.01 % 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: -0.13 (0.14), residues: 3467 helix: 1.18 (0.20), residues: 723 sheet: 0.14 (0.18), residues: 776 loop : -0.64 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 152 HIS 0.006 0.001 HIS B1048 PHE 0.021 0.001 PHE B 55 TYR 0.023 0.001 TYR H 100G ARG 0.004 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 3.197 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7613 (pmm) cc_final: 0.7146 (pmm) REVERT: A 569 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8342 (mm) REVERT: A 900 MET cc_start: 0.8242 (mtt) cc_final: 0.8011 (mtp) REVERT: H 45 LEU cc_start: 0.5186 (mt) cc_final: 0.3371 (pt) REVERT: H 59 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.5534 (m-80) REVERT: H 100 TYR cc_start: 0.8181 (t80) cc_final: 0.7879 (t80) REVERT: H 103 TRP cc_start: 0.8384 (m100) cc_final: 0.8040 (m-10) REVERT: B 389 ASP cc_start: 0.7913 (t0) cc_final: 0.7613 (t0) REVERT: B 612 TYR cc_start: 0.8393 (m-10) cc_final: 0.8037 (m-10) REVERT: B 707 TYR cc_start: 0.7324 (t80) cc_final: 0.6976 (t80) REVERT: B 886 TRP cc_start: 0.7501 (p90) cc_final: 0.6985 (p90) REVERT: C 558 LYS cc_start: 0.7472 (mttt) cc_final: 0.7136 (tppt) outliers start: 43 outliers final: 28 residues processed: 220 average time/residue: 0.3629 time to fit residues: 134.8570 Evaluate side-chains 203 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 10.0000 chunk 301 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 334 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1108 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28975 Z= 0.168 Angle : 0.527 9.872 39458 Z= 0.270 Chirality : 0.043 0.252 4685 Planarity : 0.004 0.052 5003 Dihedral : 5.440 54.074 5375 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.48 % Allowed : 12.11 % Favored : 86.41 % 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: -0.03 (0.14), residues: 3467 helix: 1.28 (0.19), residues: 723 sheet: 0.22 (0.18), residues: 770 loop : -0.60 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 152 HIS 0.005 0.001 HIS B1048 PHE 0.021 0.001 PHE C 562 TYR 0.018 0.001 TYR B1067 ARG 0.009 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 3.324 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 900 MET cc_start: 0.8300 (mtt) cc_final: 0.8043 (mtp) REVERT: A 965 GLN cc_start: 0.8879 (tp40) cc_final: 0.8601 (tp-100) REVERT: H 45 LEU cc_start: 0.5051 (mt) cc_final: 0.3358 (pt) REVERT: H 48 MET cc_start: 0.6379 (ttt) cc_final: 0.5914 (ttt) REVERT: H 59 TYR cc_start: 0.5711 (OUTLIER) cc_final: 0.5383 (m-80) REVERT: H 100 TYR cc_start: 0.8201 (t80) cc_final: 0.7861 (t80) REVERT: H 103 TRP cc_start: 0.8392 (m100) cc_final: 0.7965 (m-10) REVERT: B 389 ASP cc_start: 0.7965 (t0) cc_final: 0.7681 (t0) REVERT: B 612 TYR cc_start: 0.8453 (m-10) cc_final: 0.8165 (m-10) REVERT: B 707 TYR cc_start: 0.7338 (t80) cc_final: 0.7047 (t80) REVERT: B 740 MET cc_start: 0.8897 (ttt) cc_final: 0.8628 (ttt) REVERT: B 855 PHE cc_start: 0.7463 (m-10) cc_final: 0.7210 (m-10) outliers start: 44 outliers final: 36 residues processed: 209 average time/residue: 0.3441 time to fit residues: 122.5753 Evaluate side-chains 207 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 169 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 144 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 208 optimal weight: 0.3980 chunk 203 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A1135 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 28975 Z= 0.494 Angle : 0.713 11.396 39458 Z= 0.365 Chirality : 0.047 0.236 4685 Planarity : 0.005 0.055 5003 Dihedral : 6.461 59.566 5375 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.04 % Allowed : 11.91 % Favored : 86.05 % 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: -0.47 (0.14), residues: 3467 helix: 0.79 (0.19), residues: 730 sheet: -0.28 (0.17), residues: 822 loop : -0.72 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 152 HIS 0.008 0.002 HIS A 625 PHE 0.023 0.002 PHE B 55 TYR 0.024 0.002 TYR A 421 ARG 0.008 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 161 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8515 (m-80) cc_final: 0.8090 (m-10) REVERT: A 569 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A 902 MET cc_start: 0.9158 (mmm) cc_final: 0.8950 (mmm) REVERT: H 59 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.5496 (m-80) REVERT: H 100 TYR cc_start: 0.8352 (t80) cc_final: 0.7953 (t80) REVERT: H 103 TRP cc_start: 0.8330 (m100) cc_final: 0.7871 (m-10) REVERT: B 707 TYR cc_start: 0.7509 (t80) cc_final: 0.7142 (t80) REVERT: C 904 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.6989 (m-80) outliers start: 61 outliers final: 47 residues processed: 209 average time/residue: 0.3491 time to fit residues: 125.3689 Evaluate side-chains 202 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 212 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 764 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28975 Z= 0.170 Angle : 0.553 9.474 39458 Z= 0.284 Chirality : 0.044 0.281 4685 Planarity : 0.004 0.052 5003 Dihedral : 5.787 53.929 5375 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.45 % Allowed : 12.86 % Favored : 85.69 % 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: -0.19 (0.14), residues: 3467 helix: 1.24 (0.20), residues: 723 sheet: -0.04 (0.18), residues: 789 loop : -0.66 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 152 HIS 0.006 0.001 HIS A1048 PHE 0.025 0.001 PHE B 759 TYR 0.031 0.001 TYR L 91 ARG 0.005 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 176 time to evaluate : 3.101 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 965 GLN cc_start: 0.8901 (tp40) cc_final: 0.8674 (tp-100) REVERT: H 45 LEU cc_start: 0.5210 (mt) cc_final: 0.3399 (pt) REVERT: H 100 TYR cc_start: 0.8226 (t80) cc_final: 0.7699 (t80) REVERT: H 103 TRP cc_start: 0.8302 (m100) cc_final: 0.7978 (m-10) REVERT: L 54 ARG cc_start: 0.7236 (ptt180) cc_final: 0.6854 (ptt180) REVERT: B 389 ASP cc_start: 0.7577 (t0) cc_final: 0.7361 (t0) REVERT: B 740 MET cc_start: 0.8964 (ttt) cc_final: 0.8736 (ttt) REVERT: C 745 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7723 (p0) REVERT: C 904 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6882 (m-80) outliers start: 43 outliers final: 35 residues processed: 209 average time/residue: 0.3491 time to fit residues: 125.0011 Evaluate side-chains 206 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 0.7980 chunk 319 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 187 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 293 optimal weight: 0.9990 chunk 309 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 28975 Z= 0.162 Angle : 0.530 9.430 39458 Z= 0.273 Chirality : 0.043 0.252 4685 Planarity : 0.004 0.053 5003 Dihedral : 5.239 53.986 5375 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.35 % Allowed : 12.93 % Favored : 85.72 % 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: -0.09 (0.14), residues: 3467 helix: 1.34 (0.20), residues: 725 sheet: -0.01 (0.18), residues: 803 loop : -0.59 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.006 0.001 HIS A1048 PHE 0.025 0.001 PHE A 238 TYR 0.019 0.001 TYR L 91 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8324 (mm) REVERT: A 965 GLN cc_start: 0.8871 (tp40) cc_final: 0.8614 (tp-100) REVERT: H 45 LEU cc_start: 0.5392 (mt) cc_final: 0.3534 (pt) REVERT: H 100 TYR cc_start: 0.8261 (t80) cc_final: 0.7676 (t80) REVERT: H 103 TRP cc_start: 0.8299 (m100) cc_final: 0.7964 (m-10) REVERT: B 176 LEU cc_start: 0.6506 (tp) cc_final: 0.6259 (tp) REVERT: B 389 ASP cc_start: 0.7762 (t0) cc_final: 0.7395 (t0) REVERT: B 740 MET cc_start: 0.8938 (ttt) cc_final: 0.8722 (ttt) REVERT: C 904 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6855 (m-80) outliers start: 40 outliers final: 33 residues processed: 211 average time/residue: 0.3484 time to fit residues: 125.6356 Evaluate side-chains 206 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 6.9990 chunk 328 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 228 optimal weight: 0.0980 chunk 344 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 274 optimal weight: 0.0020 chunk 28 optimal weight: 0.7980 chunk 212 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28975 Z= 0.157 Angle : 0.523 9.292 39458 Z= 0.268 Chirality : 0.043 0.251 4685 Planarity : 0.004 0.052 5003 Dihedral : 4.904 53.599 5375 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.45 % Allowed : 13.03 % Favored : 85.53 % 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: -0.01 (0.14), residues: 3467 helix: 1.43 (0.20), residues: 727 sheet: 0.08 (0.18), residues: 787 loop : -0.56 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 36 HIS 0.006 0.001 HIS B1048 PHE 0.026 0.001 PHE A 238 TYR 0.018 0.001 TYR L 91 ARG 0.003 0.000 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 3.016 Fit side-chains revert: symmetry clash REVERT: A 569 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 965 GLN cc_start: 0.8844 (tp40) cc_final: 0.8615 (tp-100) REVERT: H 45 LEU cc_start: 0.5067 (mt) cc_final: 0.3084 (pt) REVERT: H 100 TYR cc_start: 0.8223 (t80) cc_final: 0.7793 (t80) REVERT: H 103 TRP cc_start: 0.8335 (m100) cc_final: 0.8007 (m-10) REVERT: B 389 ASP cc_start: 0.7437 (t0) cc_final: 0.7205 (t0) REVERT: B 740 MET cc_start: 0.8924 (ttt) cc_final: 0.8688 (ttt) REVERT: B 900 MET cc_start: 0.8279 (mtp) cc_final: 0.8079 (mtt) REVERT: C 904 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6813 (m-80) outliers start: 43 outliers final: 34 residues processed: 215 average time/residue: 0.3564 time to fit residues: 130.6032 Evaluate side-chains 210 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1051 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 253 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 50 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069289 restraints weight = 169255.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072120 restraints weight = 60101.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073980 restraints weight = 32799.081| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.251 28975 Z= 0.241 Angle : 0.727 59.197 39458 Z= 0.437 Chirality : 0.049 1.506 4685 Planarity : 0.005 0.165 5003 Dihedral : 4.935 53.601 5375 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.32 % Allowed : 13.42 % Favored : 85.26 % Cbeta Deviations : 0.03 % 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: -0.00 (0.14), residues: 3467 helix: 1.43 (0.20), residues: 727 sheet: 0.09 (0.18), residues: 787 loop : -0.56 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 36 HIS 0.006 0.001 HIS B1048 PHE 0.067 0.001 PHE H 63 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.82 seconds wall clock time: 93 minutes 10.70 seconds (5590.70 seconds total)