Starting phenix.real_space_refine on Mon Aug 25 12:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dbz_46739/08_2025/9dbz_46739.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dbz_46739/08_2025/9dbz_46739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dbz_46739/08_2025/9dbz_46739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dbz_46739/08_2025/9dbz_46739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dbz_46739/08_2025/9dbz_46739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dbz_46739/08_2025/9dbz_46739.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.062 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 135 5.16 5 C 17298 2.51 5 N 4368 2.21 5 O 5375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27176 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 7553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7553 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 35, 'TRANS': 989} Chain breaks: 10 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ASP:plan': 26, 'GLN:plan1': 5, 'ASN:plan1': 10, 'TYR:plan': 1, 'GLU:plan': 18, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 219 Chain: "B" Number of atoms: 8945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1210, 8945 Classifications: {'peptide': 1210} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1168} Chain breaks: 10 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 601 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASP:plan': 30, 'GLU:plan': 19, 'ARG:plan': 6, 'ASN:plan1': 8, 'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 257 Chain: "C" Number of atoms: 8698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1193, 8698 Classifications: {'peptide': 1193} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1152} Chain breaks: 14 Unresolved non-hydrogen bonds: 591 Unresolved non-hydrogen angles: 765 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'ASN:plan1': 14, 'ASP:plan': 33, 'ARG:plan': 6, 'GLN:plan1': 7, 'GLU:plan': 22, 'PHE:plan': 2, 'HIS:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 330 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "l" 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 172 Unusual residues: {'NAG': 11, 'PAM': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 186 Unusual residues: {'NAG': 12, 'PAM': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 274 Unusual residues: {'NAG': 17, 'PAM': 2} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 7.25, per 1000 atoms: 0.27 Number of scatterers: 27176 At special positions: 0 Unit cell: (187.414, 160.208, 161.216, 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 135 16.00 O 5375 8.00 N 4368 7.00 C 17298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 450 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 573 " - pdb=" SG CYS A 632 " distance=2.05 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.04 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 642 " distance=2.04 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 815 " distance=2.03 Simple disulfide: pdb=" SG CYS A 866 " - pdb=" SG CYS A 888 " distance=2.04 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 877 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1000 " distance=2.04 Simple disulfide: pdb=" SG CYS A1192 " - pdb=" SG CYS A1203 " distance=2.03 Simple disulfide: pdb=" SG CYS A1242 " - pdb=" SG CYS A1293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 450 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 405 " distance=2.04 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 498 " distance=2.04 Simple disulfide: pdb=" SG CYS B 573 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 600 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 642 " distance=2.04 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 815 " distance=2.03 Simple disulfide: pdb=" SG CYS B 866 " - pdb=" SG CYS B 888 " distance=2.03 Simple disulfide: pdb=" SG CYS B 871 " - pdb=" SG CYS B 877 " distance=2.03 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1000 " distance=2.03 Simple disulfide: pdb=" SG CYS B1192 " - pdb=" SG CYS B1203 " distance=2.03 Simple disulfide: pdb=" SG CYS B1242 " - pdb=" SG CYS B1293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 68 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 254 " - pdb=" SG CYS C 260 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 450 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 489 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 573 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 587 " - pdb=" SG CYS C 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 642 " distance=2.03 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 815 " distance=2.03 Simple disulfide: pdb=" SG CYS C 866 " - pdb=" SG CYS C 888 " distance=2.03 Simple disulfide: pdb=" SG CYS C 871 " - pdb=" SG CYS C 877 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1000 " distance=2.03 Simple disulfide: pdb=" SG CYS C1192 " - pdb=" SG CYS C1203 " distance=2.03 Simple disulfide: pdb=" SG CYS C1242 " - pdb=" SG CYS C1293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA M 3 " - " MAN M 5 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA i 3 " - " MAN i 5 " " BMA k 3 " - " MAN k 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1501 " - " ASN A 521 " " NAG A1502 " - " ASN A 537 " " NAG A1503 " - " ASN A1299 " " NAG A1504 " - " ASN A 567 " " NAG A1505 " - " ASN A 380 " " NAG A1506 " - " ASN A 410 " " NAG A1507 " - " ASN A 454 " " NAG A1508 " - " ASN A 824 " " NAG A1509 " - " ASN A 785 " " NAG A1510 " - " ASN A 339 " " NAG A1511 " - " ASN A 709 " " NAG B1501 " - " ASN B 236 " " NAG B1502 " - " ASN B 380 " " NAG B1503 " - " ASN B 521 " " NAG B1504 " - " ASN B 410 " " NAG B1505 " - " ASN B 29 " " NAG B1506 " - " ASN B 339 " " NAG B1507 " - " ASN B 785 " " NAG B1508 " - " ASN B 709 " " NAG B1509 " - " ASN B 567 " " NAG B1510 " - " ASN B 537 " " NAG B1511 " - " ASN B 67 " " NAG B1512 " - " ASN B 176 " " NAG C1502 " - " ASN C 367 " " NAG C1503 " - " ASN C 380 " " NAG C1504 " - " ASN C 824 " " NAG C1505 " - " ASN C 839 " " NAG C1506 " - " ASN C 785 " " NAG C1507 " - " ASN C 236 " " NAG C1508 " - " ASN C 537 " " NAG C1509 " - " ASN C 845 " " NAG C1510 " - " ASN C 410 " " NAG C1511 " - " ASN C 521 " " NAG C1512 " - " ASN C 567 " " NAG C1513 " - " ASN C 67 " " NAG C1514 " - " ASN C 176 " " NAG C1515 " - " ASN C 243 " " NAG C1516 " - " ASN C 339 " " NAG C1517 " - " ASN C 29 " " NAG C1518 " - " ASN C 709 " " NAG D 1 " - " ASN A 730 " " NAG E 1 " - " ASN A 926 " " NAG F 1 " - " ASN A 367 " " NAG G 1 " - " ASN A 243 " " NAG H 1 " - " ASN A 350 " " NAG I 1 " - " ASN A1079 " " NAG J 1 " - " ASN A1205 " " NAG K 1 " - " ASN A 845 " " NAG L 1 " - " ASN A 559 " " NAG M 1 " - " ASN A 290 " " NAG N 1 " - " ASN A 839 " " NAG O 1 " - " ASN B 730 " " NAG P 1 " - " ASN B 926 " " NAG Q 1 " - " ASN B 243 " " NAG R 1 " - " ASN B 824 " " NAG S 1 " - " ASN B 367 " " NAG T 1 " - " ASN B 350 " " NAG U 1 " - " ASN B 559 " " NAG V 1 " - " ASN B 845 " " NAG W 1 " - " ASN B1079 " " NAG X 1 " - " ASN B1205 " " NAG Y 1 " - " ASN B 290 " " NAG Z 1 " - " ASN B 454 " " NAG a 1 " - " ASN B1299 " " NAG b 1 " - " ASN B 210 " " NAG c 1 " - " ASN B 839 " " NAG d 1 " - " ASN C1299 " " NAG e 1 " - " ASN C 210 " " NAG f 1 " - " ASN C 559 " " NAG g 1 " - " ASN C 926 " " NAG h 1 " - " ASN C1079 " " NAG i 1 " - " ASN C 290 " " NAG j 1 " - " ASN C 454 " " NAG k 1 " - " ASN C1205 " " NAG l 1 " - " ASN C 350 " " NAG m 1 " - " ASN C 730 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 913.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6378 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 40 sheets defined 23.3% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.554A pdb=" N THR A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 874 through 882 removed outlier: 3.711A pdb=" N LYS A 879 " --> pdb=" O PRO A 875 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 880 " --> pdb=" O ARG A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 908 Processing helix chain 'A' and resid 914 through 919 removed outlier: 3.502A pdb=" N LYS A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 919 " --> pdb=" O ASN A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 914 through 919' Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 932 through 936 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 964 through 975 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.724A pdb=" N THR A 990 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1012 through 1029 Processing helix chain 'A' and resid 1043 through 1056 removed outlier: 3.511A pdb=" N ALA A1047 " --> pdb=" O PRO A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1086 Processing helix chain 'A' and resid 1099 through 1125 removed outlier: 3.667A pdb=" N LEU A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1125 " --> pdb=" O HIS A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1136 through 1144 Processing helix chain 'A' and resid 1145 through 1193 removed outlier: 3.807A pdb=" N ALA A1151 " --> pdb=" O PRO A1147 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A1156 " --> pdb=" O GLN A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1285 No H-bonds generated for 'chain 'A' and resid 1283 through 1285' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.869A pdb=" N THR B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.009A pdb=" N ILE B 159 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 491 through 501 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 865 through 871 Processing helix chain 'B' and resid 874 through 883 removed outlier: 3.672A pdb=" N LYS B 879 " --> pdb=" O PRO B 875 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 883 " --> pdb=" O LYS B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 908 removed outlier: 3.639A pdb=" N THR B 890 " --> pdb=" O SER B 886 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 920 removed outlier: 3.547A pdb=" N LEU B 919 " --> pdb=" O ASN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 950 Processing helix chain 'B' and resid 964 through 974 Processing helix chain 'B' and resid 986 through 990 removed outlier: 3.537A pdb=" N CYS B 989 " --> pdb=" O TYR B 986 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR B 990 " --> pdb=" O LYS B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 986 through 990' Processing helix chain 'B' and resid 997 through 1005 Processing helix chain 'B' and resid 1015 through 1029 Processing helix chain 'B' and resid 1043 through 1056 removed outlier: 3.556A pdb=" N ALA B1047 " --> pdb=" O PRO B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1065 through 1086 removed outlier: 4.000A pdb=" N LEU B1069 " --> pdb=" O ASN B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1124 removed outlier: 3.848A pdb=" N GLN B1115 " --> pdb=" O VAL B1111 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B1116 " --> pdb=" O VAL B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1128 removed outlier: 3.574A pdb=" N ASN B1128 " --> pdb=" O GLN B1125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1125 through 1128' Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1145 through 1193 removed outlier: 3.909A pdb=" N ALA B1151 " --> pdb=" O PRO B1147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG B1155 " --> pdb=" O ALA B1151 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B1156 " --> pdb=" O GLN B1152 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B1180 " --> pdb=" O ALA B1176 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1285 No H-bonds generated for 'chain 'B' and resid 1283 through 1285' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.688A pdb=" N CYS C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.653A pdb=" N ILE C 496 " --> pdb=" O HIS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 871 Processing helix chain 'C' and resid 874 through 882 removed outlier: 3.669A pdb=" N LYS C 879 " --> pdb=" O PRO C 875 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 880 " --> pdb=" O ARG C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.785A pdb=" N LEU C 919 " --> pdb=" O ASN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 932 through 936 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 950 Processing helix chain 'C' and resid 964 through 974 Processing helix chain 'C' and resid 997 through 1005 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.966A pdb=" N ASP C1016 " --> pdb=" O GLY C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1056 Processing helix chain 'C' and resid 1066 through 1084 Processing helix chain 'C' and resid 1099 through 1125 removed outlier: 3.703A pdb=" N LEU C1119 " --> pdb=" O GLN C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1126 through 1128 No H-bonds generated for 'chain 'C' and resid 1126 through 1128' Processing helix chain 'C' and resid 1136 through 1144 Processing helix chain 'C' and resid 1145 through 1192 removed outlier: 3.999A pdb=" N ALA C1151 " --> pdb=" O PRO C1147 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG C1155 " --> pdb=" O ALA C1151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C1156 " --> pdb=" O GLN C1152 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C1177 " --> pdb=" O THR C1173 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C1180 " --> pdb=" O ALA C1176 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1285 No H-bonds generated for 'chain 'C' and resid 1283 through 1285' Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 3.801A pdb=" N THR A 245 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 311 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 297 through 311 current: chain 'A' and resid 426 through 430 removed outlier: 3.760A pdb=" N HIS A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 437 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 440 through 444 current: chain 'A' and resid 483 through 488 Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 368 removed outlier: 8.213A pdb=" N THR A 362 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N CYS A 378 " --> pdb=" O THR A 362 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 373 through 379 current: chain 'A' and resid 412 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 508 through 513 removed outlier: 3.721A pdb=" N GLY A 757 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 751 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 525 removed outlier: 6.407A pdb=" N ASN A 521 " --> pdb=" O ASP A 693 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN A 695 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER A 523 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU A 726 " --> pdb=" O VAL A 739 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 718 " --> pdb=" O LEU A 726 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 533 through 546 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 552 through 554 current: chain 'A' and resid 598 through 599 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 598 through 599 current: chain 'A' and resid 653 through 672 Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 809 Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 827 removed outlier: 6.308A pdb=" N THR A 826 " --> pdb=" O VAL B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 838 through 843 removed outlier: 6.164A pdb=" N THR A1236 " --> pdb=" O ARG A1263 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG A1263 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A1261 " --> pdb=" O TRP A1238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 846 through 856 removed outlier: 6.024A pdb=" N LEU A1227 " --> pdb=" O HIS A1208 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS A1208 " --> pdb=" O LEU A1227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB3, first strand: chain 'A' and resid 911 through 913 Processing sheet with id=AB4, first strand: chain 'A' and resid 1287 through 1290 removed outlier: 3.756A pdb=" N HIS A1248 " --> pdb=" O ASP A1245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AB6, first strand: chain 'B' and resid 52 through 58 removed outlier: 4.105A pdb=" N TYR B 239 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 78 through 81 removed outlier: 7.308A pdb=" N PHE B 208 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N GLU B 112 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN B 210 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 106 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AB9, first strand: chain 'B' and resid 296 through 313 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 296 through 313 current: chain 'B' and resid 427 through 430 removed outlier: 3.820A pdb=" N HIS B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 443 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 437 " --> pdb=" O ASN B 441 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASN B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 440 through 444 current: chain 'B' and resid 482 through 488 Processing sheet with id=AC1, first strand: chain 'B' and resid 318 through 324 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 318 through 324 current: chain 'B' and resid 373 through 379 removed outlier: 7.620A pdb=" N CYS B 405 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR B 416 " --> pdb=" O CYS B 405 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 407 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 508 through 513 removed outlier: 3.877A pdb=" N GLY B 757 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B 771 " --> pdb=" O SER B 782 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 521 through 525 removed outlier: 6.422A pdb=" N ASN B 521 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN B 695 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER B 523 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU B 726 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR B 718 " --> pdb=" O LEU B 726 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 533 through 546 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 552 through 554 current: chain 'B' and resid 598 through 599 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 598 through 599 current: chain 'B' and resid 654 through 672 Processing sheet with id=AC5, first strand: chain 'B' and resid 807 through 809 removed outlier: 3.651A pdb=" N ILE B 807 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 838 through 843 removed outlier: 6.105A pdb=" N THR B1236 " --> pdb=" O ARG B1263 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG B1263 " --> pdb=" O THR B1236 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU B1261 " --> pdb=" O TRP B1238 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 846 through 856 removed outlier: 5.905A pdb=" N LEU B1227 " --> pdb=" O HIS B1208 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS B1208 " --> pdb=" O LEU B1227 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AC9, first strand: chain 'B' and resid 1287 through 1290 removed outlier: 3.620A pdb=" N SER B1244 " --> pdb=" O ALA B1300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 25 through 29 Processing sheet with id=AD2, first strand: chain 'C' and resid 52 through 58 removed outlier: 4.127A pdb=" N TYR C 239 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 78 through 80 removed outlier: 7.175A pdb=" N HIS C 110 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN C 210 " --> pdb=" O HIS C 108 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N HIS C 108 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 138 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 197 through 202 Processing sheet with id=AD5, first strand: chain 'C' and resid 296 through 313 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 296 through 313 current: chain 'C' and resid 426 through 430 removed outlier: 3.955A pdb=" N HIS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE C 435 " --> pdb=" O PHE C 442 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 440 through 444 current: chain 'C' and resid 482 through 488 Processing sheet with id=AD6, first strand: chain 'C' and resid 318 through 324 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 318 through 324 current: chain 'C' and resid 373 through 379 removed outlier: 7.643A pdb=" N CYS C 405 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR C 416 " --> pdb=" O CYS C 405 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 407 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 508 through 513 removed outlier: 3.686A pdb=" N GLY C 757 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 771 " --> pdb=" O SER C 782 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 521 through 525 removed outlier: 6.466A pdb=" N ASN C 521 " --> pdb=" O ASP C 693 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN C 695 " --> pdb=" O ASN C 521 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER C 523 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 736 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 726 " --> pdb=" O VAL C 739 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 727 " --> pdb=" O TYR C 718 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 533 through 546 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 552 through 554 current: chain 'C' and resid 598 through 599 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 598 through 599 current: chain 'C' and resid 654 through 672 Processing sheet with id=AE1, first strand: chain 'C' and resid 807 through 809 removed outlier: 3.632A pdb=" N ILE C 807 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 838 through 856 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 838 through 856 current: chain 'C' and resid 1219 through 1238 removed outlier: 5.777A pdb=" N THR C1236 " --> pdb=" O ARG C1263 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG C1263 " --> pdb=" O THR C1236 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU C1261 " --> pdb=" O TRP C1238 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AE4, first strand: chain 'C' and resid 1287 through 1290 882 hydrogen bonds defined for protein. 2454 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: 5.73 Time building geometry restraints manager: 3.34 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: 4392 1.32 - 1.46: 10481 1.46 - 1.59: 12614 1.59 - 1.73: 0 1.73 - 1.87: 172 Bond restraints: 27659 Sorted by residual: bond pdb=" N VAL B 313 " pdb=" CA VAL B 313 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.30e-03 1.88e+04 1.82e+01 bond pdb=" C ASN B1205 " pdb=" O ASN B1205 " ideal model delta sigma weight residual 1.235 1.188 0.048 1.23e-02 6.61e+03 1.50e+01 bond pdb=" C GLN B 356 " pdb=" O GLN B 356 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.26e-02 6.30e+03 1.39e+01 bond pdb=" N VAL C 517 " pdb=" CA VAL C 517 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.07e+01 bond pdb=" N VAL B 520 " pdb=" CA VAL B 520 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.15e-02 7.56e+03 9.89e+00 ... (remaining 27654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 37299 2.62 - 5.24: 431 5.24 - 7.86: 30 7.86 - 10.48: 0 10.48 - 13.10: 2 Bond angle restraints: 37762 Sorted by residual: angle pdb=" CA CYS A 632 " pdb=" CB CYS A 632 " pdb=" SG CYS A 632 " ideal model delta sigma weight residual 114.40 127.50 -13.10 2.30e+00 1.89e-01 3.25e+01 angle pdb=" CA ASN B 290 " pdb=" CB ASN B 290 " pdb=" CG ASN B 290 " ideal model delta sigma weight residual 112.60 117.70 -5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" N ASN B 290 " pdb=" CA ASN B 290 " pdb=" C ASN B 290 " ideal model delta sigma weight residual 112.88 106.37 6.51 1.29e+00 6.01e-01 2.54e+01 angle pdb=" CA ASN C 290 " pdb=" CB ASN C 290 " pdb=" CG ASN C 290 " ideal model delta sigma weight residual 112.60 117.52 -4.92 1.00e+00 1.00e+00 2.42e+01 angle pdb=" CA ILE B 140 " pdb=" C ILE B 140 " pdb=" O ILE B 140 " ideal model delta sigma weight residual 122.63 118.39 4.24 8.70e-01 1.32e+00 2.38e+01 ... (remaining 37757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 16779 21.41 - 42.82: 810 42.82 - 64.23: 142 64.23 - 85.64: 83 85.64 - 107.05: 41 Dihedral angle restraints: 17855 sinusoidal: 7905 harmonic: 9950 Sorted by residual: dihedral pdb=" CB CYS C 324 " pdb=" SG CYS C 324 " pdb=" SG CYS C 450 " pdb=" CB CYS C 450 " ideal model delta sinusoidal sigma weight residual 93.00 9.43 83.57 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS A 573 " pdb=" SG CYS A 573 " pdb=" SG CYS A 632 " pdb=" CB CYS A 632 " ideal model delta sinusoidal sigma weight residual 93.00 17.14 75.86 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS B 803 " pdb=" SG CYS B 803 " pdb=" SG CYS B 815 " pdb=" CB CYS B 815 " ideal model delta sinusoidal sigma weight residual 93.00 167.33 -74.33 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 17852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 4729 0.147 - 0.294: 46 0.294 - 0.441: 6 0.441 - 0.588: 1 0.588 - 0.735: 1 Chirality restraints: 4783 Sorted by residual: chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 1.67 0.73 2.00e-02 2.50e+03 1.35e+03 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.89 0.49 2.00e-02 2.50e+03 6.11e+02 chirality pdb=" C1 BMA l 3 " pdb=" O4 NAG l 2 " pdb=" C2 BMA l 3 " pdb=" O5 BMA l 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.63e+02 ... (remaining 4780 not shown) Planarity restraints: 4720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.157 2.00e-02 2.50e+03 1.29e-01 2.10e+02 pdb=" C7 NAG T 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " 0.118 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.095 2.00e-02 2.50e+03 8.04e-02 8.08e+01 pdb=" C7 NAG W 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " -0.025 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.128 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.091 2.00e-02 2.50e+03 7.71e-02 7.42e+01 pdb=" C7 NAG M 1 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.123 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.074 2.00e-02 2.50e+03 ... (remaining 4717 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5166 2.78 - 3.31: 22587 3.31 - 3.84: 43029 3.84 - 4.37: 52087 4.37 - 4.90: 89969 Nonbonded interactions: 212838 Sorted by model distance: nonbonded pdb=" OG1 THR A 700 " pdb=" OD1 ASP B1139 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN B 380 " pdb=" OH TYR B 389 " model vdw 2.248 3.040 nonbonded pdb=" O GLN A 506 " pdb=" OH TYR A 510 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN C 380 " pdb=" OH TYR C 389 " model vdw 2.261 3.040 nonbonded pdb=" OE1 GLU C 426 " pdb=" O HOH C1601 " model vdw 2.263 3.040 ... (remaining 212833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 40 through 42 and (name N or name CA or name C or name O \ or name CB )) or resid 43 through 49 or (resid 50 through 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 258 or (resid 259 and \ (name N or name CA or name C or name O or name CB )) or resid 260 through 262 or \ (resid 263 through 264 and (name N or name CA or name C or name O or name CB )) \ or resid 265 through 364 or (resid 365 and (name N or name CA or name C or name \ O or name CB )) or resid 366 through 367 or (resid 368 through 369 and (name N \ or name CA or name C or name O or name CB )) or resid 370 through 382 or resid 3 \ 97 or resid 401 through 483 or (resid 484 and (name N or name CA or name C or na \ me O or name CB )) or resid 485 through 498 or (resid 499 and (name N or name CA \ or name C or name O or name CB )) or resid 500 through 501 or (resid 502 throug \ h 504 and (name N or name CA or name C or name O or name CB )) or resid 505 thro \ ugh 528 or (resid 529 through 530 and (name N or name CA or name C or name O or \ name CB )) or resid 531 or (resid 532 and (name N or name CA or name C or name O \ or name CB )) or resid 533 or (resid 534 and (name N or name CA or name C or na \ me O or name CB )) or resid 535 through 540 or (resid 541 and (name N or name CA \ or name C or name O or name CB )) or resid 542 through 544 or (resid 545 and (n \ ame N or name CA or name C or name O or name CB )) or resid 546 through 550 or ( \ resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 567 or (resid 568 through 569 and (name N or name CA or name C or name O \ or name CB )) or resid 570 through 585 or (resid 586 and (name N or name CA or \ name C or name O or name CB )) or resid 587 through 589 or (resid 590 through 59 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 592 through \ 594 or (resid 595 and (name N or name CA or name C or name O or name CB )) or re \ sid 596 through 602 or (resid 603 and (name N or name CA or name C or name O or \ name CB )) or resid 604 through 606 or (resid 607 through 608 and (name N or nam \ e CA or name C or name O or name CB )) or resid 609 through 617 or (resid 618 an \ d (name N or name CA or name C or name O or name CB )) or resid 619 through 633 \ or (resid 634 and (name N or name CA or name C or name O or name CB )) or resid \ 635 through 637 or (resid 638 and (name N or name CA or name C or name O or name \ CB )) or resid 639 through 644 or (resid 645 and (name N or name CA or name C o \ r name O or name CB )) or resid 646 through 650 or (resid 651 through 652 and (n \ ame N or name CA or name C or name O or name CB )) or resid 653 through 665 or ( \ resid 666 and (name N or name CA or name C or name O or name CB )) or resid 667 \ through 688 or (resid 689 through 690 and (name N or name CA or name C or name O \ or name CB )) or resid 691 through 711 or (resid 712 and (name N or name CA or \ name C or name O or name CB )) or resid 713 or (resid 714 and (name N or name CA \ or name C or name O or name CB )) or resid 715 through 723 or (resid 724 and (n \ ame N or name CA or name C or name O or name CB )) or resid 725 through 730 or ( \ resid 731 through 733 and (name N or name CA or name C or name O or name CB )) o \ r resid 734 or (resid 735 and (name N or name CA or name C or name O or name CB \ )) or resid 736 through 764 or (resid 765 and (name N or name CA or name C or na \ me O or name CB )) or resid 766 through 787 or resid 801 through 807 or (resid 8 \ 08 and (name N or name CA or name C or name O or name CB )) or resid 809 through \ 882 or (resid 883 and (name N or name CA or name C or name O or name CB )) or r \ esid 884 through 892 or (resid 893 through 894 and (name N or name CA or name C \ or name O or name CB )) or resid 895 through 904 or (resid 905 and (name N or na \ me CA or name C or name O or name CB )) or resid 906 or (resid 907 and (name N o \ r name CA or name C or name O or name CB )) or resid 908 through 973 or (resid 9 \ 74 through 983 and (name N or name CA or name C or name O or name CB )) or resid \ 984 through 1016 or (resid 1017 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1018 through 1114 or (resid 1115 and (name N or name CA or na \ me C or name O or name CB )) or resid 1116 through 1168 or (resid 1169 and (name \ N or name CA or name C or name O or name CB )) or resid 1170 through 1186 or (r \ esid 1187 and (name N or name CA or name C or name O or name CB )) or resid 1188 \ through 1196 or (resid 1197 through 1198 and (name N or name CA or name C or na \ me O or name CB )) or resid 1199 through 1245 or (resid 1248 through 1249 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1250 through 1266 or \ (resid 1267 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 268 through 1307 or resid 1502 through 1511)) selection = (chain 'C' and ((resid 40 through 42 and (name N or name CA or name C or name O \ or name CB )) or resid 43 through 45 or (resid 46 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and \ (name N or name CA or name C or name O or name CB )) or resid 57 or (resid 238 a \ nd (name N or name CA or name C or name O or name CB )) or resid 239 or (resid 2 \ 40 through 241 and (name N or name CA or name C or name O or name CB )) or resid \ 242 through 245 or (resid 246 and (name N or name CA or name C or name O or nam \ e CB )) or resid 247 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 252 or (resid 253 and (name N or na \ me CA or name C or name O or name CB )) or resid 254 through 260 or (resid 261 a \ nd (name N or name CA or name C or name O or name CB )) or resid 262 through 271 \ or (resid 272 and (name N or name CA or name C or name O or name CB )) or resid \ 273 through 280 or (resid 281 and (name N or name CA or name C or name O or nam \ e CB )) or resid 282 through 288 or (resid 289 and (name N or name CA or name C \ or name O or name CB )) or resid 290 through 291 or (resid 292 through 293 and ( \ name N or name CA or name C or name O or name CB )) or resid 294 or (resid 295 t \ hrough 296 and (name N or name CA or name C or name O or name CB )) or resid 297 \ through 300 or (resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 312 or resid 322 through 327 or (resid 330 through 332 \ and (name N or name CA or name C or name O or name CB )) or resid 333 through 33 \ 9 or (resid 340 through 341 and (name N or name CA or name C or name O or name C \ B )) or resid 342 through 348 or (resid 349 and (name N or name CA or name C or \ name O or name CB )) or resid 350 through 354 or (resid 355 through 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 374 or (re \ sid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 th \ rough 380 or (resid 381 through 382 and (name N or name CA or name C or name O o \ r name CB )) or resid 392 or resid 401 through 418 or (resid 419 and (name N or \ name CA or name C or name O or name CB )) or resid 420 through 422 or (resid 423 \ and (name N or name CA or name C or name O or name CB )) or resid 424 through 4 \ 25 or (resid 426 and (name N or name CA or name C or name O or name CB )) or res \ id 427 through 429 or (resid 430 and (name N or name CA or name C or name O or n \ ame CB )) or resid 431 through 448 or (resid 449 and (name N or name CA or name \ C or name O or name CB )) or resid 450 through 451 or (resid 452 and (name N or \ name CA or name C or name O or name CB )) or resid 453 through 456 or resid 461 \ through 479 or (resid 480 and (name N or name CA or name C or name O or name CB \ )) or resid 481 through 590 or (resid 591 and (name N or name CA or name C or na \ me O or name CB )) or resid 592 through 658 or (resid 659 and (name N or name CA \ or name C or name O or name CB )) or resid 660 through 674 or resid 685 through \ 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or r \ esid 753 through 787 or resid 801 through 815 or (resid 816 and (name N or name \ CA or name C or name O or name CB )) or resid 817 through 822 or (resid 823 and \ (name N or name CA or name C or name O or name CB )) or resid 824 through 881 or \ (resid 882 through 883 and (name N or name CA or name C or name O or name CB )) \ or resid 884 through 928 or (resid 929 and (name N or name CA or name C or name \ O or name CB )) or resid 930 through 931 or (resid 932 and (name N or name CA o \ r name C or name O or name CB )) or resid 933 through 957 or (resid 958 through \ 959 and (name N or name CA or name C or name O or name CB )) or resid 960 throug \ h 971 or (resid 972 and (name N or name CA or name C or name O or name CB )) or \ resid 973 through 1059 or (resid 1060 through 1061 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1062 through 1123 or (resid 1124 and (name \ N or name CA or name C or name O or name CB )) or resid 1125 through 1138 or (re \ sid 1139 and (name N or name CA or name C or name O or name CB )) or resid 1140 \ through 1197 or (resid 1198 and (name N or name CA or name C or name O or name C \ B )) or resid 1199 through 1307 or resid 1502 through 1511)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' selection = chain 'm' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'W' selection = chain 'h' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.960 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 27844 Z= 0.269 Angle : 0.850 52.266 38268 Z= 0.406 Chirality : 0.053 0.735 4783 Planarity : 0.005 0.129 4644 Dihedral : 14.613 107.048 11330 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.68 % Allowed : 10.28 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3354 helix: 0.52 (0.19), residues: 724 sheet: 0.38 (0.17), residues: 917 loop : -0.87 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 298 TYR 0.015 0.001 TYR B 718 PHE 0.015 0.001 PHE B 88 TRP 0.024 0.001 TRP B 201 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00469 (27659) covalent geometry : angle 0.65943 (37762) SS BOND : bond 0.00493 ( 49) SS BOND : angle 1.53477 ( 98) hydrogen bonds : bond 0.17735 ( 882) hydrogen bonds : angle 6.28864 ( 2454) link_ALPHA1-3 : bond 0.04841 ( 7) link_ALPHA1-3 : angle 4.47275 ( 21) link_ALPHA1-6 : bond 0.04582 ( 7) link_ALPHA1-6 : angle 12.28594 ( 21) link_BETA1-4 : bond 0.03618 ( 46) link_BETA1-4 : angle 6.52687 ( 138) link_NAG-ASN : bond 0.00592 ( 76) link_NAG-ASN : angle 2.61187 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8217 (t80) REVERT: B 803 CYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5783 (t) REVERT: B 822 PHE cc_start: 0.8140 (m-80) cc_final: 0.7617 (t80) REVERT: B 1054 TYR cc_start: 0.8599 (t80) cc_final: 0.8164 (t80) REVERT: B 1170 GLN cc_start: 0.8760 (tt0) cc_final: 0.8558 (mt0) REVERT: C 179 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.5979 (mtpp) REVERT: C 201 TRP cc_start: 0.7622 (m-90) cc_final: 0.6655 (t60) REVERT: C 900 ARG cc_start: 0.8637 (ttt90) cc_final: 0.8378 (ttp-110) outliers start: 41 outliers final: 33 residues processed: 246 average time/residue: 0.4290 time to fit residues: 128.2263 Evaluate side-chains 234 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 1021 MET Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1013 VAL Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1067 GLN Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 944 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1148 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1165 ASN A1208 HIS A1214 ASN B 84 HIS B 200 ASN B 308 ASN B 872 ASN B1005 ASN B1082 GLN B1129 ASN B1183 GLN B1208 HIS C 334 ASN C 565 GLN C1067 GLN C1142 ASN C1183 GLN C1198 GLN C1208 HIS C1214 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103912 restraints weight = 31408.178| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.45 r_work: 0.2994 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27844 Z= 0.112 Angle : 0.551 10.368 38268 Z= 0.270 Chirality : 0.044 0.287 4783 Planarity : 0.003 0.046 4644 Dihedral : 9.853 80.982 6570 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.05 % Allowed : 10.65 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.14), residues: 3354 helix: 1.35 (0.19), residues: 739 sheet: 0.40 (0.17), residues: 889 loop : -0.71 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.013 0.001 TYR A 436 PHE 0.013 0.001 PHE A1210 TRP 0.009 0.001 TRP B 592 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00238 (27659) covalent geometry : angle 0.50915 (37762) SS BOND : bond 0.00395 ( 49) SS BOND : angle 1.18342 ( 98) hydrogen bonds : bond 0.05679 ( 882) hydrogen bonds : angle 4.91251 ( 2454) link_ALPHA1-3 : bond 0.01439 ( 7) link_ALPHA1-3 : angle 1.67091 ( 21) link_ALPHA1-6 : bond 0.00649 ( 7) link_ALPHA1-6 : angle 1.98096 ( 21) link_BETA1-4 : bond 0.00599 ( 46) link_BETA1-4 : angle 2.29384 ( 138) link_NAG-ASN : bond 0.00294 ( 76) link_NAG-ASN : angle 1.90872 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8178 (t80) REVERT: A 564 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7632 (tmm) REVERT: A 897 MET cc_start: 0.8873 (tpp) cc_final: 0.8630 (tpp) REVERT: B 1170 GLN cc_start: 0.8773 (tt0) cc_final: 0.8558 (mt0) REVERT: C 179 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.5881 (mtpp) REVERT: C 201 TRP cc_start: 0.7494 (m-90) cc_final: 0.6618 (t60) REVERT: C 692 THR cc_start: 0.8833 (p) cc_final: 0.8628 (p) REVERT: C 900 ARG cc_start: 0.8742 (ttt90) cc_final: 0.8386 (ttp-110) outliers start: 50 outliers final: 27 residues processed: 246 average time/residue: 0.4761 time to fit residues: 141.9773 Evaluate side-chains 222 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 12 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 119 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 283 optimal weight: 0.0370 chunk 217 optimal weight: 4.9990 chunk 199 optimal weight: 0.0770 overall best weight: 1.0378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A1170 GLN B 81 ASN C1067 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101194 restraints weight = 31579.880| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.36 r_work: 0.2946 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27844 Z= 0.140 Angle : 0.561 11.910 38268 Z= 0.276 Chirality : 0.045 0.271 4783 Planarity : 0.004 0.047 4644 Dihedral : 8.864 80.122 6536 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 10.73 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3354 helix: 1.59 (0.20), residues: 737 sheet: 0.40 (0.17), residues: 877 loop : -0.70 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 298 TYR 0.015 0.001 TYR B 718 PHE 0.013 0.001 PHE B 443 TRP 0.008 0.001 TRP B 432 HIS 0.003 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00325 (27659) covalent geometry : angle 0.52240 (37762) SS BOND : bond 0.00526 ( 49) SS BOND : angle 1.37455 ( 98) hydrogen bonds : bond 0.06066 ( 882) hydrogen bonds : angle 4.82498 ( 2454) link_ALPHA1-3 : bond 0.01210 ( 7) link_ALPHA1-3 : angle 1.75943 ( 21) link_ALPHA1-6 : bond 0.00669 ( 7) link_ALPHA1-6 : angle 1.65934 ( 21) link_BETA1-4 : bond 0.00495 ( 46) link_BETA1-4 : angle 2.18145 ( 138) link_NAG-ASN : bond 0.00233 ( 76) link_NAG-ASN : angle 1.86164 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8198 (t80) REVERT: A 564 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7701 (tmm) REVERT: A 897 MET cc_start: 0.8850 (tpp) cc_final: 0.8579 (tpt) REVERT: B 1021 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8955 (mtm) REVERT: B 1155 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8456 (mtt180) REVERT: B 1170 GLN cc_start: 0.8818 (tt0) cc_final: 0.8558 (mt0) REVERT: C 179 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.5902 (mtpp) REVERT: C 201 TRP cc_start: 0.7560 (m-90) cc_final: 0.6607 (t60) REVERT: C 298 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8063 (ttp-170) REVERT: C 900 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8475 (ttp-110) outliers start: 65 outliers final: 43 residues processed: 245 average time/residue: 0.4116 time to fit residues: 124.2342 Evaluate side-chains 246 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 450 CYS Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1013 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 276 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 304 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN B 81 ASN C1067 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101598 restraints weight = 31392.725| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.33 r_work: 0.2971 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27844 Z= 0.147 Angle : 0.566 11.122 38268 Z= 0.279 Chirality : 0.045 0.261 4783 Planarity : 0.004 0.048 4644 Dihedral : 8.188 76.556 6535 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 10.73 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.14), residues: 3354 helix: 1.66 (0.20), residues: 736 sheet: 0.40 (0.17), residues: 879 loop : -0.73 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1199 TYR 0.015 0.001 TYR B 718 PHE 0.013 0.001 PHE B 443 TRP 0.018 0.001 TRP B 201 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00345 (27659) covalent geometry : angle 0.52712 (37762) SS BOND : bond 0.00594 ( 49) SS BOND : angle 1.59252 ( 98) hydrogen bonds : bond 0.06065 ( 882) hydrogen bonds : angle 4.77109 ( 2454) link_ALPHA1-3 : bond 0.01258 ( 7) link_ALPHA1-3 : angle 1.82304 ( 21) link_ALPHA1-6 : bond 0.00775 ( 7) link_ALPHA1-6 : angle 1.62591 ( 21) link_BETA1-4 : bond 0.00484 ( 46) link_BETA1-4 : angle 2.09617 ( 138) link_NAG-ASN : bond 0.00215 ( 76) link_NAG-ASN : angle 1.84201 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8202 (t80) REVERT: A 564 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7614 (tmm) REVERT: A 897 MET cc_start: 0.8847 (tpp) cc_final: 0.8513 (tpp) REVERT: B 1021 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8886 (mtm) REVERT: B 1054 TYR cc_start: 0.8567 (t80) cc_final: 0.8116 (t80) REVERT: B 1155 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8397 (mtt180) REVERT: B 1170 GLN cc_start: 0.8813 (tt0) cc_final: 0.8528 (mt0) REVERT: C 179 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.5926 (mtpp) REVERT: C 201 TRP cc_start: 0.7534 (m-90) cc_final: 0.6617 (t60) REVERT: C 298 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8062 (ttp-170) REVERT: C 900 ARG cc_start: 0.8770 (ttt90) cc_final: 0.8493 (ttp-110) outliers start: 69 outliers final: 47 residues processed: 247 average time/residue: 0.4597 time to fit residues: 138.4166 Evaluate side-chains 246 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1013 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 325 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 300 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN B 81 ASN C1067 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101751 restraints weight = 31320.615| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.38 r_work: 0.2970 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27844 Z= 0.158 Angle : 0.581 11.637 38268 Z= 0.286 Chirality : 0.045 0.282 4783 Planarity : 0.004 0.048 4644 Dihedral : 8.013 77.751 6533 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.83 % Allowed : 11.22 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.14), residues: 3354 helix: 1.62 (0.20), residues: 742 sheet: 0.37 (0.17), residues: 879 loop : -0.75 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 298 TYR 0.015 0.001 TYR B 718 PHE 0.014 0.001 PHE B 443 TRP 0.017 0.001 TRP B 201 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00372 (27659) covalent geometry : angle 0.54097 (37762) SS BOND : bond 0.00607 ( 49) SS BOND : angle 1.74971 ( 98) hydrogen bonds : bond 0.06217 ( 882) hydrogen bonds : angle 4.78100 ( 2454) link_ALPHA1-3 : bond 0.01260 ( 7) link_ALPHA1-3 : angle 1.87334 ( 21) link_ALPHA1-6 : bond 0.00806 ( 7) link_ALPHA1-6 : angle 1.61939 ( 21) link_BETA1-4 : bond 0.00475 ( 46) link_BETA1-4 : angle 2.04365 ( 138) link_NAG-ASN : bond 0.00257 ( 76) link_NAG-ASN : angle 1.93262 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8170 (t80) REVERT: A 564 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7579 (tmm) REVERT: A 897 MET cc_start: 0.8793 (tpp) cc_final: 0.8444 (tpp) REVERT: B 1021 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8890 (mtm) REVERT: B 1054 TYR cc_start: 0.8572 (t80) cc_final: 0.8103 (t80) REVERT: B 1155 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8390 (mtt180) REVERT: B 1170 GLN cc_start: 0.8805 (tt0) cc_final: 0.8487 (mt0) REVERT: C 179 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.5913 (mtpp) REVERT: C 201 TRP cc_start: 0.7456 (m-90) cc_final: 0.6527 (t60) REVERT: C 298 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8037 (ttp-170) REVERT: C 900 ARG cc_start: 0.8768 (ttt90) cc_final: 0.8427 (ttp-110) outliers start: 69 outliers final: 53 residues processed: 243 average time/residue: 0.4174 time to fit residues: 124.2445 Evaluate side-chains 252 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1013 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 253 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN C1067 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100910 restraints weight = 31574.061| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.23 r_work: 0.2928 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27844 Z= 0.159 Angle : 0.574 11.358 38268 Z= 0.283 Chirality : 0.045 0.248 4783 Planarity : 0.004 0.049 4644 Dihedral : 7.768 75.703 6533 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.15 % Allowed : 11.22 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3354 helix: 1.61 (0.20), residues: 743 sheet: 0.35 (0.17), residues: 877 loop : -0.77 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 298 TYR 0.015 0.001 TYR B 718 PHE 0.015 0.001 PHE A 48 TRP 0.022 0.001 TRP B 201 HIS 0.004 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00376 (27659) covalent geometry : angle 0.53819 (37762) SS BOND : bond 0.00638 ( 49) SS BOND : angle 1.51144 ( 98) hydrogen bonds : bond 0.06264 ( 882) hydrogen bonds : angle 4.77560 ( 2454) link_ALPHA1-3 : bond 0.01253 ( 7) link_ALPHA1-3 : angle 1.88145 ( 21) link_ALPHA1-6 : bond 0.00852 ( 7) link_ALPHA1-6 : angle 1.57236 ( 21) link_BETA1-4 : bond 0.00458 ( 46) link_BETA1-4 : angle 1.96868 ( 138) link_NAG-ASN : bond 0.00252 ( 76) link_NAG-ASN : angle 1.88102 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 201 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8219 (t80) REVERT: A 564 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7675 (tmm) REVERT: A 897 MET cc_start: 0.8910 (tpp) cc_final: 0.8540 (tpp) REVERT: B 822 PHE cc_start: 0.8108 (m-80) cc_final: 0.7662 (t80) REVERT: B 1054 TYR cc_start: 0.8627 (t80) cc_final: 0.8154 (t80) REVERT: B 1155 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8443 (mtt180) REVERT: B 1170 GLN cc_start: 0.8920 (tt0) cc_final: 0.8598 (mt0) REVERT: C 201 TRP cc_start: 0.7474 (m-90) cc_final: 0.6564 (t60) REVERT: C 298 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8084 (ttp-170) REVERT: C 900 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8519 (ttp-110) outliers start: 77 outliers final: 55 residues processed: 249 average time/residue: 0.3969 time to fit residues: 121.6458 Evaluate side-chains 254 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1120 SER Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 653 ASN Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1013 VAL Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 900 ARG Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 318 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 0.0070 chunk 303 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN C 108 HIS C 110 HIS C1067 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103288 restraints weight = 31348.311| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.28 r_work: 0.2997 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 27844 Z= 0.109 Angle : 0.527 13.126 38268 Z= 0.261 Chirality : 0.044 0.252 4783 Planarity : 0.003 0.046 4644 Dihedral : 7.211 73.606 6529 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.21 % Allowed : 12.12 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.14), residues: 3354 helix: 1.84 (0.20), residues: 744 sheet: 0.39 (0.17), residues: 886 loop : -0.66 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 298 TYR 0.013 0.001 TYR A 718 PHE 0.014 0.001 PHE A1210 TRP 0.012 0.001 TRP A 432 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00240 (27659) covalent geometry : angle 0.49363 (37762) SS BOND : bond 0.00537 ( 49) SS BOND : angle 1.55994 ( 98) hydrogen bonds : bond 0.05151 ( 882) hydrogen bonds : angle 4.56837 ( 2454) link_ALPHA1-3 : bond 0.01285 ( 7) link_ALPHA1-3 : angle 1.79598 ( 21) link_ALPHA1-6 : bond 0.00920 ( 7) link_ALPHA1-6 : angle 1.43560 ( 21) link_BETA1-4 : bond 0.00472 ( 46) link_BETA1-4 : angle 1.78443 ( 138) link_NAG-ASN : bond 0.00261 ( 76) link_NAG-ASN : angle 1.68450 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8117 (t80) REVERT: A 564 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: A 607 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8770 (t) REVERT: A 897 MET cc_start: 0.8872 (tpp) cc_final: 0.8478 (tpp) REVERT: B 822 PHE cc_start: 0.8078 (m-80) cc_final: 0.7662 (t80) REVERT: B 1155 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8348 (mtt180) REVERT: B 1170 GLN cc_start: 0.8812 (tt0) cc_final: 0.8565 (mt0) REVERT: C 179 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.5850 (mtpp) REVERT: C 201 TRP cc_start: 0.7405 (m-90) cc_final: 0.6507 (t60) REVERT: C 298 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8048 (ttp-170) REVERT: C 900 ARG cc_start: 0.8757 (ttt90) cc_final: 0.8424 (ttp-110) outliers start: 54 outliers final: 39 residues processed: 240 average time/residue: 0.3951 time to fit residues: 115.9025 Evaluate side-chains 242 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 31 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 312 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN C1067 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103118 restraints weight = 31448.187| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.36 r_work: 0.2955 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27844 Z= 0.122 Angle : 0.535 11.845 38268 Z= 0.265 Chirality : 0.044 0.256 4783 Planarity : 0.003 0.047 4644 Dihedral : 7.072 73.221 6529 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.42 % Allowed : 11.96 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.14), residues: 3354 helix: 1.84 (0.20), residues: 744 sheet: 0.40 (0.17), residues: 877 loop : -0.68 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.014 0.001 TYR B 718 PHE 0.016 0.001 PHE C 253 TRP 0.014 0.001 TRP A 432 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00277 (27659) covalent geometry : angle 0.50120 (37762) SS BOND : bond 0.00522 ( 49) SS BOND : angle 1.55279 ( 98) hydrogen bonds : bond 0.05425 ( 882) hydrogen bonds : angle 4.58489 ( 2454) link_ALPHA1-3 : bond 0.01242 ( 7) link_ALPHA1-3 : angle 1.84581 ( 21) link_ALPHA1-6 : bond 0.00930 ( 7) link_ALPHA1-6 : angle 1.42381 ( 21) link_BETA1-4 : bond 0.00451 ( 46) link_BETA1-4 : angle 1.79239 ( 138) link_NAG-ASN : bond 0.00233 ( 76) link_NAG-ASN : angle 1.70803 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8142 (t80) REVERT: A 564 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7538 (tmm) REVERT: A 607 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8765 (t) REVERT: A 897 MET cc_start: 0.8880 (tpp) cc_final: 0.8510 (tpt) REVERT: B 214 MET cc_start: 0.6726 (mtt) cc_final: 0.6415 (mmt) REVERT: B 822 PHE cc_start: 0.8092 (m-80) cc_final: 0.7652 (t80) REVERT: B 1155 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8320 (mtt180) REVERT: B 1170 GLN cc_start: 0.8832 (tt0) cc_final: 0.8576 (mt0) REVERT: C 179 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.5830 (mtpp) REVERT: C 201 TRP cc_start: 0.7396 (m-90) cc_final: 0.6486 (t60) REVERT: C 298 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8003 (ttp-170) REVERT: C 900 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8459 (ttp-110) REVERT: C 1123 THR cc_start: 0.8874 (m) cc_final: 0.8610 (m) outliers start: 59 outliers final: 44 residues processed: 235 average time/residue: 0.4344 time to fit residues: 124.4433 Evaluate side-chains 247 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 777 ASN Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 803 CYS Chi-restraints excluded: chain C residue 900 ARG Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 81 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 217 optimal weight: 0.0870 chunk 204 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 329 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A1115 GLN C 110 HIS C1067 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104502 restraints weight = 31618.444| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.36 r_work: 0.3018 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27844 Z= 0.099 Angle : 0.497 9.299 38268 Z= 0.247 Chirality : 0.043 0.242 4783 Planarity : 0.003 0.046 4644 Dihedral : 6.636 69.560 6529 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.92 % Allowed : 12.49 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3354 helix: 1.98 (0.20), residues: 745 sheet: 0.39 (0.17), residues: 897 loop : -0.57 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.012 0.001 TYR C1022 PHE 0.016 0.001 PHE C 253 TRP 0.020 0.001 TRP B 201 HIS 0.003 0.000 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00214 (27659) covalent geometry : angle 0.46744 (37762) SS BOND : bond 0.00469 ( 49) SS BOND : angle 1.26613 ( 98) hydrogen bonds : bond 0.04748 ( 882) hydrogen bonds : angle 4.44864 ( 2454) link_ALPHA1-3 : bond 0.01235 ( 7) link_ALPHA1-3 : angle 1.76258 ( 21) link_ALPHA1-6 : bond 0.01003 ( 7) link_ALPHA1-6 : angle 1.35703 ( 21) link_BETA1-4 : bond 0.00471 ( 46) link_BETA1-4 : angle 1.66963 ( 138) link_NAG-ASN : bond 0.00240 ( 76) link_NAG-ASN : angle 1.57511 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 607 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8759 (t) REVERT: A 897 MET cc_start: 0.8822 (tpp) cc_final: 0.8465 (tpp) REVERT: B 214 MET cc_start: 0.6778 (mtt) cc_final: 0.6503 (mmt) REVERT: B 822 PHE cc_start: 0.7999 (m-80) cc_final: 0.7596 (t80) REVERT: B 1155 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8278 (mtt180) REVERT: B 1170 GLN cc_start: 0.8761 (tt0) cc_final: 0.8555 (mt0) REVERT: C 179 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.5819 (mtpp) REVERT: C 201 TRP cc_start: 0.7423 (m-90) cc_final: 0.6488 (t60) REVERT: C 900 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8435 (ttp-110) REVERT: C 1123 THR cc_start: 0.8779 (m) cc_final: 0.8552 (m) outliers start: 47 outliers final: 38 residues processed: 238 average time/residue: 0.4325 time to fit residues: 126.1963 Evaluate side-chains 243 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 900 ARG Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 232 optimal weight: 0.0040 chunk 146 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A1115 GLN B1117 GLN C 110 HIS C1067 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.138348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103624 restraints weight = 31269.292| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.30 r_work: 0.2995 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27844 Z= 0.115 Angle : 0.517 9.702 38268 Z= 0.257 Chirality : 0.044 0.231 4783 Planarity : 0.003 0.047 4644 Dihedral : 6.621 70.044 6529 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.29 % Allowed : 12.33 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.14), residues: 3354 helix: 1.96 (0.20), residues: 744 sheet: 0.41 (0.17), residues: 874 loop : -0.63 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.013 0.001 TYR C1022 PHE 0.018 0.001 PHE B 253 TRP 0.017 0.001 TRP A 432 HIS 0.003 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00260 (27659) covalent geometry : angle 0.48640 (37762) SS BOND : bond 0.00489 ( 49) SS BOND : angle 1.36814 ( 98) hydrogen bonds : bond 0.05185 ( 882) hydrogen bonds : angle 4.50269 ( 2454) link_ALPHA1-3 : bond 0.01199 ( 7) link_ALPHA1-3 : angle 1.79231 ( 21) link_ALPHA1-6 : bond 0.00974 ( 7) link_ALPHA1-6 : angle 1.34619 ( 21) link_BETA1-4 : bond 0.00444 ( 46) link_BETA1-4 : angle 1.69712 ( 138) link_NAG-ASN : bond 0.00222 ( 76) link_NAG-ASN : angle 1.61791 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6708 Ramachandran restraints generated. 3354 Oldfield, 0 Emsley, 3354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 607 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8773 (t) REVERT: A 897 MET cc_start: 0.8889 (tpp) cc_final: 0.8472 (tpp) REVERT: B 214 MET cc_start: 0.6796 (mtt) cc_final: 0.6538 (mmt) REVERT: B 822 PHE cc_start: 0.8026 (m-80) cc_final: 0.7598 (t80) REVERT: B 1155 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8338 (mtt180) REVERT: B 1170 GLN cc_start: 0.8807 (tt0) cc_final: 0.8577 (mt0) REVERT: C 179 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.5831 (mtpp) REVERT: C 201 TRP cc_start: 0.7447 (m-90) cc_final: 0.6519 (t60) REVERT: C 900 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8470 (ttp-110) REVERT: C 1123 THR cc_start: 0.8805 (m) cc_final: 0.8585 (m) outliers start: 56 outliers final: 43 residues processed: 239 average time/residue: 0.4170 time to fit residues: 121.6819 Evaluate side-chains 249 residues out of total 2963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 549 TYR Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1154 ASP Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 TYR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 564 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1155 ARG Chi-restraints excluded: chain B residue 1221 ILE Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 549 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 900 ARG Chi-restraints excluded: chain C residue 944 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1148 SER Chi-restraints excluded: chain C residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 337 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 258 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 219 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A1115 GLN B1117 GLN C 110 HIS C1067 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104213 restraints weight = 31115.124| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.34 r_work: 0.3007 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27844 Z= 0.107 Angle : 0.507 9.126 38268 Z= 0.252 Chirality : 0.043 0.237 4783 Planarity : 0.003 0.047 4644 Dihedral : 6.480 68.290 6529 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.13 % Allowed : 12.53 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.14), residues: 3354 helix: 2.01 (0.20), residues: 744 sheet: 0.42 (0.17), residues: 876 loop : -0.60 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 298 TYR 0.013 0.001 TYR A 718 PHE 0.017 0.001 PHE C 253 TRP 0.021 0.001 TRP B 201 HIS 0.003 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00237 (27659) covalent geometry : angle 0.47763 (37762) SS BOND : bond 0.00472 ( 49) SS BOND : angle 1.33324 ( 98) hydrogen bonds : bond 0.05007 ( 882) hydrogen bonds : angle 4.46886 ( 2454) link_ALPHA1-3 : bond 0.01200 ( 7) link_ALPHA1-3 : angle 1.75130 ( 21) link_ALPHA1-6 : bond 0.00984 ( 7) link_ALPHA1-6 : angle 1.32225 ( 21) link_BETA1-4 : bond 0.00449 ( 46) link_BETA1-4 : angle 1.64863 ( 138) link_NAG-ASN : bond 0.00224 ( 76) link_NAG-ASN : angle 1.57392 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9091.66 seconds wall clock time: 155 minutes 11.45 seconds (9311.45 seconds total)