Starting phenix.real_space_refine on Mon May 4 11:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z9l_73949/05_2026/9z9l_73949.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z9l_73949/05_2026/9z9l_73949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z9l_73949/05_2026/9z9l_73949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z9l_73949/05_2026/9z9l_73949.map" model { file = "/net/cci-nas-00/data/ceres_data/9z9l_73949/05_2026/9z9l_73949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z9l_73949/05_2026/9z9l_73949.cif" } resolution = 3.49 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= -0.052 sd= 0.387 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 119 5.16 5 C 12853 2.51 5 N 3358 2.21 5 O 4165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20495 Number of models: 1 Model: "" Number of chains: 50 Chain: "E" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1015 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 836 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1015 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 796 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 96} Chain: "K" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1049 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 769 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain breaks: 1 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3486 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1012 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 973 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "C" Number of atoms: 3504 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3495 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 441, 3495 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 bond proxies already assigned to first conformer: 3558 Chain: "G" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3469 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 2, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Z" 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: "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: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "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: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 5.84, per 1000 atoms: 0.28 Number of scatterers: 20495 At special positions: 0 Unit cell: (130.72, 153.94, 185.76, 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 119 16.00 O 4165 8.00 N 3358 7.00 C 12853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.16 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 91 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 31 " distance=2.18 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 100 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.18 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 89 " - pdb=" SG CYS L 96 " distance=2.06 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.14 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.05 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS C 501 " distance=2.12 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 605 " - pdb=" SG CYS G 501 " distance=2.13 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.21 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.22 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.30 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.17 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.05 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Z 4 " - " MAN Z 5 " " MAN h 4 " - " MAN h 5 " " MAN l 4 " - " MAN l 5 " ALPHA1-3 " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA X 6 " - " MAN X 7 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA h 3 " - " MAN h 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 7 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 6 " - " MAN Y 7 " " BMA h 3 " - " MAN h 6 " " MAN h 6 " - " MAN h 7 " " BMA j 3 " - " MAN j 5 " BETA1-4 " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " 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 j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " BETA1-6 " NAG V 1 " - " FUC V 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 4 " " BMA X 3 " - " BMA X 6 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 448 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 133 " " NAG A 605 " - " ASN A 465 " " NAG A 606 " - " ASN A 241 " " NAG A 607 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 339 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG G 601 " - " ASN G 301 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 392 " " NAG G 604 " - " ASN G 448 " " NAG G 605 " - " ASN G 241 " " NAG I 701 " - " ASN I 625 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 234 " " NAG V 1 " - " ASN B 625 " " NAG W 1 " - " ASN D 625 " " NAG X 1 " - " ASN C 88 " " NAG Y 1 " - " ASN C 160 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 301 " " NAG c 1 " - " ASN C 332 " " NAG d 1 " - " ASN C 197 " " NAG e 1 " - " ASN C 386 " " NAG f 1 " - " ASN C 448 " " NAG g 1 " - " ASN C 234 " " NAG h 1 " - " ASN C 156 " " NAG i 1 " - " ASN C 465 " " NAG j 1 " - " ASN G 88 " " NAG k 1 " - " ASN G 156 " " NAG l 1 " - " ASN G 262 " " NAG m 1 " - " ASN G 332 " " NAG n 1 " - " ASN G 386 " " NAG o 1 " - " ASN G 197 " " NAG p 1 " - " ASN G 234 " " NAG q 1 " - " ASN G 465 " " NAG r 1 " - " ASN G 160 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4412 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 37 sheets defined 20.8% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.574A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.505A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.668A pdb=" N ASN K 31 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.247A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.675A pdb=" N THR A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.585A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.609A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.801A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.637A pdb=" N LYS B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.637A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.514A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.529A pdb=" N LYS D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.536A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 597 Processing helix chain 'I' and resid 618 through 624 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 654 Processing helix chain 'I' and resid 655 through 658 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.552A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.911A pdb=" N TYR C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.638A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.541A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 25 current: chain 'E' and resid 73 through 82 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 58 current: chain 'E' and resid 100F through 103 Processing sheet with id=AA3, first strand: chain 'F' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 9 through 14 current: chain 'F' and resid 48 through 52 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 56 through 57 current: chain 'F' and resid 98 through 102 Processing sheet with id=AA4, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 27 current: chain 'H' and resid 73 through 82 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100F through 103 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 54 through 55 removed outlier: 6.761A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N TYR J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR J 98 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.780A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 100 through 104 removed outlier: 4.156A pdb=" N TYR K 102 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER K 114 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N ILE K 104 " --> pdb=" O GLN K 112 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N GLN K 112 " --> pdb=" O ILE K 104 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS K 110 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS C 171 " --> pdb=" O HIS K 110 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLN K 112 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N TYR C 173 " --> pdb=" O GLN K 112 " (cutoff:3.500A) removed outlier: 13.810A pdb=" N SER K 114 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 20.501A pdb=" N LEU C 175 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 26.184A pdb=" N THR K 116 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 30.806A pdb=" N TYR C 177 " --> pdb=" O THR K 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 11 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.506A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.997A pdb=" N HIS A 66 " --> pdb=" O SER A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.697A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.403A pdb=" N THR A 293 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A 334 " --> pdb=" O THR A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AC5, first strand: chain 'A' and resid 301 through 307 removed outlier: 4.288A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.328A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 603 through 609 removed outlier: 8.333A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.633A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.865A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.994A pdb=" N HIS C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.284A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 4.355A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AD5, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.489A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'G' and resid 201 through 203 removed outlier: 6.382A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 309 removed outlier: 4.091A pdb=" N ASN G 301 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 323 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 530 hydrogen bonds defined for protein. 1383 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: 3.55 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5694 1.33 - 1.46: 6124 1.46 - 1.60: 8956 1.60 - 1.73: 0 1.73 - 1.86: 154 Bond restraints: 20928 Sorted by residual: bond pdb=" CB HIS L 93 " pdb=" CG HIS L 93 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.47e+01 bond pdb=" N TRP J 36 " pdb=" CA TRP J 36 " ideal model delta sigma weight residual 1.454 1.514 -0.060 1.23e-02 6.61e+03 2.35e+01 bond pdb=" CA ALA J 35 " pdb=" C ALA J 35 " ideal model delta sigma weight residual 1.521 1.578 -0.057 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C TYR C 173 " pdb=" CA BTYR C 173 " ideal model delta sigma weight residual 1.521 1.572 -0.051 1.19e-02 7.06e+03 1.83e+01 bond pdb=" N ALA J 35 " pdb=" CA ALA J 35 " ideal model delta sigma weight residual 1.455 1.500 -0.046 1.26e-02 6.30e+03 1.31e+01 ... (remaining 20923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 25860 2.27 - 4.54: 2110 4.54 - 6.80: 394 6.80 - 9.07: 47 9.07 - 11.34: 11 Bond angle restraints: 28422 Sorted by residual: angle pdb=" C ARG A 469 " pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta sigma weight residual 119.87 128.36 -8.49 1.04e+00 9.25e-01 6.66e+01 angle pdb=" C GLU G 492 " pdb=" N PRO G 493 " pdb=" CA PRO G 493 " ideal model delta sigma weight residual 119.56 127.88 -8.32 1.02e+00 9.61e-01 6.66e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 127.83 -8.27 1.02e+00 9.61e-01 6.58e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.61 -8.05 1.02e+00 9.61e-01 6.24e+01 angle pdb=" C THR C 219 " pdb=" N PRO C 220 " pdb=" CA PRO C 220 " ideal model delta sigma weight residual 119.78 127.81 -8.03 1.03e+00 9.43e-01 6.07e+01 ... (remaining 28417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.39: 13534 22.39 - 44.79: 302 44.79 - 67.18: 73 67.18 - 89.58: 102 89.58 - 111.97: 58 Dihedral angle restraints: 14069 sinusoidal: 7196 harmonic: 6873 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -176.04 90.04 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS L 89 " pdb=" SG CYS L 89 " pdb=" SG CYS L 96 " pdb=" CB CYS L 96 " ideal model delta sinusoidal sigma weight residual -86.00 -175.88 89.88 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS F 92 " pdb=" SG CYS F 92 " pdb=" SG CYS F 100 " pdb=" CB CYS F 100 " ideal model delta sinusoidal sigma weight residual 93.00 160.26 -67.26 1 1.00e+01 1.00e-02 5.89e+01 ... (remaining 14066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 3481 0.220 - 0.439: 35 0.439 - 0.659: 4 0.659 - 0.879: 0 0.879 - 1.098: 1 Chirality restraints: 3521 Sorted by residual: chirality pdb=" C1 MAN X 5 " pdb=" O2 MAN X 4 " pdb=" C2 MAN X 5 " pdb=" O5 MAN X 5 " both_signs ideal model delta sigma weight residual False 2.40 1.30 1.10 2.00e-02 2.50e+03 3.02e+03 chirality pdb=" C1 MAN M 6 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 6 " pdb=" O5 MAN M 6 " both_signs ideal model delta sigma weight residual False 2.40 1.81 0.59 2.00e-02 2.50e+03 8.62e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.07e+02 ... (remaining 3518 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 2 " 0.312 2.00e-02 2.50e+03 2.63e-01 8.67e+02 pdb=" C7 NAG r 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG r 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG r 2 " -0.454 2.00e-02 2.50e+03 pdb=" O7 NAG r 2 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 1 " -0.279 2.00e-02 2.50e+03 2.33e-01 6.79e+02 pdb=" C7 NAG r 1 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG r 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG r 1 " 0.393 2.00e-02 2.50e+03 pdb=" O7 NAG r 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 2 " -0.127 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C7 NAG Q 2 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG Q 2 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG Q 2 " 0.167 2.00e-02 2.50e+03 pdb=" O7 NAG Q 2 " 0.024 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 376 2.67 - 3.23: 18931 3.23 - 3.79: 29523 3.79 - 4.34: 40593 4.34 - 4.90: 66441 Nonbonded interactions: 155864 Sorted by model distance: nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 2.117 3.040 nonbonded pdb=" C3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 2.248 3.470 nonbonded pdb=" O4 NAG T 2 " pdb=" O6 NAG T 2 " model vdw 2.275 3.040 nonbonded pdb=" OG SER H 100A" pdb=" O4 MAN X 4 " model vdw 2.320 3.040 nonbonded pdb=" O3 NAG l 2 " pdb=" O5 BMA l 3 " model vdw 2.355 3.040 ... (remaining 155859 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 34 through 172 or resid 174 through 506 or resid 603)) selection = (chain 'C' and (resid 34 through 59 or resid 66 through 172 or resid 174 through \ 506 or resid 603)) selection = (chain 'G' and (resid 34 through 172 or resid 174 through 601)) } ncs_group { reference = (chain 'B' and (resid 520 through 543 or resid 570 through 659 or resid 702)) selection = (chain 'D' and (resid 520 through 543 or resid 570 through 659 or resid 702)) selection = (chain 'I' and (resid 520 through 543 or resid 570 through 701)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = (chain 'F' and (resid 2 through 23 or resid 34 through 112)) selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 1 or resid 4 or resid 6)) selection = (chain 'Q' and (resid 2 or resid 5 or resid 7)) selection = (chain 'X' and (resid 2 or resid 5 or resid 7)) selection = (chain 'Y' and (resid 2 or resid 5 or resid 7)) selection = (chain 'h' and (resid 2 or resid 5 or resid 7)) } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) } ncs_group { reference = (chain 'W' and resid 1 through 3) selection = (chain 'r' and resid 1 through 3) } ncs_group { reference = chain 'Z' selection = chain 'j' 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=0.50 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: 7.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.320 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.014 0.271 21095 Z= 0.732 Angle : 1.460 12.924 28881 Z= 0.889 Chirality : 0.078 1.098 3521 Planarity : 0.008 0.263 3431 Dihedral : 14.607 111.974 9531 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.37 % Favored : 98.59 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % 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 are not related in a simple way. whole: 2.29 (0.17), residues: 2341 helix: -0.15 (0.21), residues: 420 sheet: 1.93 (0.19), residues: 664 loop : 2.18 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.033 0.004 TYR A 40 PHE 0.039 0.004 PHE J 34 TRP 0.029 0.005 TRP G 69 HIS 0.019 0.001 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.01295 (20928) covalent geometry : angle 1.40315 (28422) SS BOND : bond 0.07868 ( 42) SS BOND : angle 3.90374 ( 84) hydrogen bonds : bond 0.22559 ( 530) hydrogen bonds : angle 6.94272 ( 1383) link_ALPHA1-2 : bond 0.00590 ( 7) link_ALPHA1-2 : angle 3.61222 ( 21) link_ALPHA1-3 : bond 0.01994 ( 11) link_ALPHA1-3 : angle 4.13034 ( 33) link_ALPHA1-6 : bond 0.01389 ( 7) link_ALPHA1-6 : angle 1.19855 ( 21) link_BETA1-4 : bond 0.01553 ( 45) link_BETA1-4 : angle 3.31807 ( 135) link_BETA1-6 : bond 0.00937 ( 3) link_BETA1-6 : angle 3.08089 ( 9) link_NAG-ASN : bond 0.06531 ( 52) link_NAG-ASN : angle 3.46032 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 ILE cc_start: 0.7914 (mt) cc_final: 0.7655 (mm) REVERT: F 56 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7633 (tt0) REVERT: F 75 TYR cc_start: 0.7531 (m-80) cc_final: 0.7224 (m-80) REVERT: H 100 SER cc_start: 0.7759 (p) cc_final: 0.7494 (p) REVERT: J 36 TRP cc_start: 0.7832 (m100) cc_final: 0.7424 (m100) REVERT: L 51 ASP cc_start: 0.8040 (t0) cc_final: 0.7691 (t0) REVERT: A 80 ASN cc_start: 0.8202 (m-40) cc_final: 0.7847 (p0) REVERT: B 634 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7041 (tp30) REVERT: I 625 ASN cc_start: 0.6882 (t0) cc_final: 0.6563 (t0) REVERT: I 626 MET cc_start: 0.7900 (mtp) cc_final: 0.7694 (mtm) REVERT: C 66 HIS cc_start: 0.8024 (m-70) cc_final: 0.7544 (m-70) REVERT: C 78 ASP cc_start: 0.8685 (m-30) cc_final: 0.8471 (m-30) REVERT: C 475 MET cc_start: 0.8845 (mmm) cc_final: 0.8466 (tpt) REVERT: G 35 TRP cc_start: 0.7430 (m100) cc_final: 0.6946 (m-10) REVERT: G 45 TRP cc_start: 0.7050 (p90) cc_final: 0.6841 (p90) REVERT: G 377 ASN cc_start: 0.7465 (t0) cc_final: 0.7245 (p0) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.1889 time to fit residues: 125.4782 Evaluate side-chains 317 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN H 105 GLN J 43 GLN ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 ASN A 130 HIS A 249 HIS B 607 ASN I 540 GLN I 575 GLN I 577 GLN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS G 85 HIS G 287 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.060034 restraints weight = 71960.084| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.14 r_work: 0.2682 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21095 Z= 0.180 Angle : 0.780 11.640 28881 Z= 0.379 Chirality : 0.048 0.216 3521 Planarity : 0.005 0.048 3431 Dihedral : 12.083 96.331 5116 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Rotamer: Outliers : 1.96 % Allowed : 5.55 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % 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 are not related in a simple way. whole: 1.87 (0.17), residues: 2341 helix: 1.70 (0.27), residues: 393 sheet: 1.52 (0.18), residues: 709 loop : 1.08 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 504 TYR 0.023 0.002 TYR L 72 PHE 0.022 0.002 PHE G 159 TRP 0.026 0.002 TRP L 38 HIS 0.010 0.002 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00394 (20928) covalent geometry : angle 0.72094 (28422) SS BOND : bond 0.00888 ( 42) SS BOND : angle 1.37034 ( 84) hydrogen bonds : bond 0.06995 ( 530) hydrogen bonds : angle 5.47940 ( 1383) link_ALPHA1-2 : bond 0.01683 ( 7) link_ALPHA1-2 : angle 2.22573 ( 21) link_ALPHA1-3 : bond 0.01200 ( 11) link_ALPHA1-3 : angle 2.64014 ( 33) link_ALPHA1-6 : bond 0.00932 ( 7) link_ALPHA1-6 : angle 2.02683 ( 21) link_BETA1-4 : bond 0.00474 ( 45) link_BETA1-4 : angle 2.29494 ( 135) link_BETA1-6 : bond 0.00987 ( 3) link_BETA1-6 : angle 1.90702 ( 9) link_NAG-ASN : bond 0.00523 ( 52) link_NAG-ASN : angle 3.07466 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 374 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8459 (tt0) REVERT: F 56 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7983 (pt0) REVERT: F 69 LYS cc_start: 0.7784 (tptm) cc_final: 0.7456 (tptm) REVERT: H 82 ASN cc_start: 0.7270 (t0) cc_final: 0.7063 (t0) REVERT: H 100 SER cc_start: 0.7844 (p) cc_final: 0.7528 (p) REVERT: J 36 TRP cc_start: 0.7759 (m100) cc_final: 0.7521 (m100) REVERT: L 36 TYR cc_start: 0.7833 (m-80) cc_final: 0.7612 (m-80) REVERT: A 80 ASN cc_start: 0.8366 (m-40) cc_final: 0.8039 (p0) REVERT: A 268 LYS cc_start: 0.8918 (tppt) cc_final: 0.8669 (ttmm) REVERT: D 542 ARG cc_start: 0.8471 (mtp180) cc_final: 0.8123 (mtp180) REVERT: D 639 THR cc_start: 0.8605 (m) cc_final: 0.8390 (p) REVERT: D 664 ASP cc_start: 0.8288 (t70) cc_final: 0.7580 (t0) REVERT: G 195 ASN cc_start: 0.7922 (p0) cc_final: 0.7638 (p0) REVERT: G 377 ASN cc_start: 0.7634 (t0) cc_final: 0.7161 (p0) REVERT: G 396 TYR cc_start: 0.8588 (m-80) cc_final: 0.8281 (m-10) outliers start: 41 outliers final: 18 residues processed: 390 average time/residue: 0.1773 time to fit residues: 102.5730 Evaluate side-chains 351 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 333 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain G residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 154 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 228 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN ** I 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.058689 restraints weight = 69182.866| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.06 r_work: 0.2650 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21095 Z= 0.159 Angle : 0.717 11.945 28881 Z= 0.350 Chirality : 0.046 0.213 3521 Planarity : 0.004 0.056 3431 Dihedral : 10.531 94.842 5116 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 1.87 % Allowed : 7.47 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 1.52 (0.17), residues: 2341 helix: 2.05 (0.28), residues: 386 sheet: 1.58 (0.19), residues: 687 loop : 0.44 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 45 TYR 0.021 0.002 TYR L 72 PHE 0.018 0.002 PHE C 383 TRP 0.027 0.002 TRP G 45 HIS 0.009 0.002 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00356 (20928) covalent geometry : angle 0.66652 (28422) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.16544 ( 84) hydrogen bonds : bond 0.06473 ( 530) hydrogen bonds : angle 5.17809 ( 1383) link_ALPHA1-2 : bond 0.01213 ( 7) link_ALPHA1-2 : angle 2.39165 ( 21) link_ALPHA1-3 : bond 0.01060 ( 11) link_ALPHA1-3 : angle 2.21832 ( 33) link_ALPHA1-6 : bond 0.00809 ( 7) link_ALPHA1-6 : angle 2.06336 ( 21) link_BETA1-4 : bond 0.00428 ( 45) link_BETA1-4 : angle 1.91394 ( 135) link_BETA1-6 : bond 0.01135 ( 3) link_BETA1-6 : angle 2.36838 ( 9) link_NAG-ASN : bond 0.00310 ( 52) link_NAG-ASN : angle 2.74936 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 358 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 56 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8019 (tt0) REVERT: H 100 SER cc_start: 0.7955 (p) cc_final: 0.7548 (t) REVERT: K 70 MET cc_start: 0.7288 (ttt) cc_final: 0.6662 (ttt) REVERT: L 53 GLU cc_start: 0.8727 (mp0) cc_final: 0.8364 (mp0) REVERT: A 80 ASN cc_start: 0.8402 (m-40) cc_final: 0.8020 (p0) REVERT: A 268 LYS cc_start: 0.8946 (tppt) cc_final: 0.8736 (ttmm) REVERT: D 542 ARG cc_start: 0.8469 (mtp180) cc_final: 0.8253 (mtp180) REVERT: D 664 ASP cc_start: 0.8347 (t70) cc_final: 0.7687 (t0) REVERT: I 607 ASN cc_start: 0.7376 (m-40) cc_final: 0.6992 (m110) REVERT: G 45 TRP cc_start: 0.7163 (p90) cc_final: 0.6938 (p90) outliers start: 39 outliers final: 26 residues processed: 377 average time/residue: 0.1745 time to fit residues: 97.6364 Evaluate side-chains 350 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 45 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 GLN C 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.070562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.056131 restraints weight = 85988.854| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.45 r_work: 0.2578 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21095 Z= 0.173 Angle : 0.711 10.039 28881 Z= 0.350 Chirality : 0.047 0.230 3521 Planarity : 0.005 0.057 3431 Dihedral : 9.459 90.726 5116 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 2.58 % Allowed : 8.66 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 1.18 (0.17), residues: 2341 helix: 2.00 (0.28), residues: 386 sheet: 1.49 (0.19), residues: 698 loop : 0.02 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 500 TYR 0.022 0.002 TYR F 52 PHE 0.024 0.002 PHE C 383 TRP 0.023 0.002 TRP J 36 HIS 0.009 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00397 (20928) covalent geometry : angle 0.66500 (28422) SS BOND : bond 0.00479 ( 42) SS BOND : angle 1.23274 ( 84) hydrogen bonds : bond 0.06399 ( 530) hydrogen bonds : angle 5.09836 ( 1383) link_ALPHA1-2 : bond 0.01164 ( 7) link_ALPHA1-2 : angle 2.38612 ( 21) link_ALPHA1-3 : bond 0.01053 ( 11) link_ALPHA1-3 : angle 2.33905 ( 33) link_ALPHA1-6 : bond 0.00829 ( 7) link_ALPHA1-6 : angle 1.97241 ( 21) link_BETA1-4 : bond 0.00393 ( 45) link_BETA1-4 : angle 1.87658 ( 135) link_BETA1-6 : bond 0.01246 ( 3) link_BETA1-6 : angle 2.71352 ( 9) link_NAG-ASN : bond 0.00349 ( 52) link_NAG-ASN : angle 2.51758 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 GLU cc_start: 0.6924 (tp30) cc_final: 0.6516 (tp30) REVERT: F 45 ARG cc_start: 0.8286 (mpp80) cc_final: 0.8021 (mpp80) REVERT: F 56 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8135 (tt0) REVERT: H 100 SER cc_start: 0.8023 (p) cc_final: 0.7751 (t) REVERT: J 36 TRP cc_start: 0.7894 (m100) cc_final: 0.7512 (m100) REVERT: K 70 MET cc_start: 0.7344 (ttt) cc_final: 0.6803 (ttt) REVERT: L 53 GLU cc_start: 0.8775 (mp0) cc_final: 0.8376 (mp0) REVERT: A 80 ASN cc_start: 0.8502 (m-40) cc_final: 0.8090 (p0) REVERT: I 607 ASN cc_start: 0.7406 (m-40) cc_final: 0.7103 (m110) REVERT: C 46 ARG cc_start: 0.8653 (ptm-80) cc_final: 0.8371 (ptm-80) REVERT: C 473 SER cc_start: 0.8333 (p) cc_final: 0.7780 (t) REVERT: C 504 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8777 (mtt180) REVERT: G 45 TRP cc_start: 0.7218 (p90) cc_final: 0.6744 (p90) outliers start: 54 outliers final: 35 residues processed: 376 average time/residue: 0.1696 time to fit residues: 95.5449 Evaluate side-chains 366 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN G 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.063086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.049709 restraints weight = 64364.871| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.86 r_work: 0.2524 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2402 r_free = 0.2402 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2402 r_free = 0.2402 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 21095 Z= 0.264 Angle : 0.837 10.818 28881 Z= 0.416 Chirality : 0.051 0.232 3521 Planarity : 0.006 0.064 3431 Dihedral : 9.490 85.676 5116 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 2.92 % Allowed : 9.00 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.49 (0.16), residues: 2341 helix: 1.45 (0.27), residues: 395 sheet: 1.21 (0.19), residues: 687 loop : -0.55 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 327 TYR 0.024 0.003 TYR F 52 PHE 0.042 0.003 PHE C 383 TRP 0.032 0.003 TRP L 35 HIS 0.012 0.003 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00639 (20928) covalent geometry : angle 0.78831 (28422) SS BOND : bond 0.00623 ( 42) SS BOND : angle 1.60833 ( 84) hydrogen bonds : bond 0.08025 ( 530) hydrogen bonds : angle 5.41048 ( 1383) link_ALPHA1-2 : bond 0.01201 ( 7) link_ALPHA1-2 : angle 2.40691 ( 21) link_ALPHA1-3 : bond 0.00933 ( 11) link_ALPHA1-3 : angle 2.45169 ( 33) link_ALPHA1-6 : bond 0.00811 ( 7) link_ALPHA1-6 : angle 2.10292 ( 21) link_BETA1-4 : bond 0.00413 ( 45) link_BETA1-4 : angle 2.05264 ( 135) link_BETA1-6 : bond 0.01427 ( 3) link_BETA1-6 : angle 3.24246 ( 9) link_NAG-ASN : bond 0.00507 ( 52) link_NAG-ASN : angle 2.86377 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 336 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8652 (tt0) REVERT: F 34 LYS cc_start: 0.8841 (mppt) cc_final: 0.8554 (mppt) REVERT: F 56 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8224 (tt0) REVERT: H 100 SER cc_start: 0.8347 (p) cc_final: 0.8094 (p) REVERT: J 36 TRP cc_start: 0.8054 (m100) cc_final: 0.7678 (m100) REVERT: L 35 TRP cc_start: 0.8326 (m100) cc_final: 0.8117 (m100) REVERT: A 80 ASN cc_start: 0.8799 (m-40) cc_final: 0.8419 (p0) REVERT: I 607 ASN cc_start: 0.7475 (m-40) cc_final: 0.7150 (m110) REVERT: C 473 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8155 (t) REVERT: C 504 ARG cc_start: 0.9168 (ttm-80) cc_final: 0.8909 (mtt-85) REVERT: G 45 TRP cc_start: 0.7367 (p90) cc_final: 0.6670 (p90) REVERT: G 396 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8323 (m-10) outliers start: 61 outliers final: 44 residues processed: 363 average time/residue: 0.1671 time to fit residues: 91.1319 Evaluate side-chains 366 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.056128 restraints weight = 64196.784| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.94 r_work: 0.2583 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2466 r_free = 0.2466 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21095 Z= 0.141 Angle : 0.671 9.828 28881 Z= 0.329 Chirality : 0.045 0.222 3521 Planarity : 0.004 0.063 3431 Dihedral : 8.728 83.257 5116 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 2.44 % Allowed : 10.05 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.65 (0.17), residues: 2341 helix: 1.87 (0.28), residues: 387 sheet: 1.11 (0.19), residues: 708 loop : -0.43 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.041 0.001 TYR F 52 PHE 0.016 0.002 PHE J 99 TRP 0.018 0.001 TRP G 35 HIS 0.006 0.001 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00310 (20928) covalent geometry : angle 0.62594 (28422) SS BOND : bond 0.00600 ( 42) SS BOND : angle 1.11676 ( 84) hydrogen bonds : bond 0.05876 ( 530) hydrogen bonds : angle 5.10164 ( 1383) link_ALPHA1-2 : bond 0.01076 ( 7) link_ALPHA1-2 : angle 2.45598 ( 21) link_ALPHA1-3 : bond 0.01088 ( 11) link_ALPHA1-3 : angle 2.16445 ( 33) link_ALPHA1-6 : bond 0.00859 ( 7) link_ALPHA1-6 : angle 1.89599 ( 21) link_BETA1-4 : bond 0.00427 ( 45) link_BETA1-4 : angle 1.75911 ( 135) link_BETA1-6 : bond 0.01176 ( 3) link_BETA1-6 : angle 2.59742 ( 9) link_NAG-ASN : bond 0.00271 ( 52) link_NAG-ASN : angle 2.45989 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 96 LEU cc_start: 0.8380 (tp) cc_final: 0.7943 (tp) REVERT: F 34 LYS cc_start: 0.8846 (mppt) cc_final: 0.8497 (mppt) REVERT: F 56 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8302 (tt0) REVERT: H 100 SER cc_start: 0.8363 (p) cc_final: 0.8060 (t) REVERT: J 36 TRP cc_start: 0.7993 (m100) cc_final: 0.7646 (m100) REVERT: J 92 TYR cc_start: 0.5406 (m-10) cc_final: 0.5165 (m-10) REVERT: K 6 GLU cc_start: 0.7982 (mp0) cc_final: 0.7427 (mt-10) REVERT: L 51 ASP cc_start: 0.8430 (t0) cc_final: 0.8204 (t0) REVERT: L 53 GLU cc_start: 0.8887 (mp0) cc_final: 0.8635 (mp0) REVERT: A 80 ASN cc_start: 0.8783 (m-40) cc_final: 0.8414 (p0) REVERT: C 340 LYS cc_start: 0.6264 (mmtm) cc_final: 0.6048 (mmtm) REVERT: C 473 SER cc_start: 0.8508 (p) cc_final: 0.7975 (t) REVERT: C 504 ARG cc_start: 0.9142 (ttm-80) cc_final: 0.8881 (mtt180) REVERT: G 35 TRP cc_start: 0.6939 (m-10) cc_final: 0.6496 (m-10) REVERT: G 45 TRP cc_start: 0.7364 (p90) cc_final: 0.6334 (p90) REVERT: G 396 TYR cc_start: 0.8710 (m-10) cc_final: 0.8264 (m-80) REVERT: G 475 MET cc_start: 0.9241 (mmt) cc_final: 0.8442 (mmt) outliers start: 51 outliers final: 35 residues processed: 363 average time/residue: 0.1711 time to fit residues: 92.9747 Evaluate side-chains 361 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 65 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain I residue 652 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 97 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN G 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.069707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.055852 restraints weight = 71537.695| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.13 r_work: 0.2570 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21095 Z= 0.150 Angle : 0.677 9.542 28881 Z= 0.334 Chirality : 0.046 0.222 3521 Planarity : 0.004 0.065 3431 Dihedral : 8.333 80.600 5116 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.84 % Rotamer: Outliers : 2.25 % Allowed : 10.58 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 1.92 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.62 (0.17), residues: 2341 helix: 1.92 (0.28), residues: 387 sheet: 1.10 (0.19), residues: 708 loop : -0.49 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.037 0.002 TYR F 52 PHE 0.018 0.002 PHE C 383 TRP 0.022 0.001 TRP L 35 HIS 0.006 0.001 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00338 (20928) covalent geometry : angle 0.63285 (28422) SS BOND : bond 0.00427 ( 42) SS BOND : angle 1.44221 ( 84) hydrogen bonds : bond 0.05921 ( 530) hydrogen bonds : angle 5.03181 ( 1383) link_ALPHA1-2 : bond 0.01137 ( 7) link_ALPHA1-2 : angle 2.41921 ( 21) link_ALPHA1-3 : bond 0.01071 ( 11) link_ALPHA1-3 : angle 2.11895 ( 33) link_ALPHA1-6 : bond 0.00841 ( 7) link_ALPHA1-6 : angle 1.76885 ( 21) link_BETA1-4 : bond 0.00413 ( 45) link_BETA1-4 : angle 1.74582 ( 135) link_BETA1-6 : bond 0.01204 ( 3) link_BETA1-6 : angle 2.70108 ( 9) link_NAG-ASN : bond 0.00271 ( 52) link_NAG-ASN : angle 2.38121 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 335 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8115 (ttp80) REVERT: F 34 LYS cc_start: 0.8737 (mppt) cc_final: 0.8379 (mppt) REVERT: F 56 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8355 (tt0) REVERT: H 100 SER cc_start: 0.8209 (p) cc_final: 0.7846 (t) REVERT: J 36 TRP cc_start: 0.7760 (m100) cc_final: 0.7425 (m100) REVERT: K 6 GLU cc_start: 0.7863 (mp0) cc_final: 0.7542 (mt-10) REVERT: L 51 ASP cc_start: 0.8186 (t0) cc_final: 0.7932 (t0) REVERT: L 53 GLU cc_start: 0.8723 (mp0) cc_final: 0.8397 (mp0) REVERT: A 80 ASN cc_start: 0.8611 (m-40) cc_final: 0.8330 (p0) REVERT: C 340 LYS cc_start: 0.6140 (mmtm) cc_final: 0.5918 (mmtm) REVERT: C 473 SER cc_start: 0.8317 (p) cc_final: 0.7846 (t) REVERT: C 504 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8767 (mtt180) REVERT: G 35 TRP cc_start: 0.7096 (m-10) cc_final: 0.6882 (m-10) REVERT: G 45 TRP cc_start: 0.7273 (p90) cc_final: 0.6491 (p90) outliers start: 47 outliers final: 37 residues processed: 359 average time/residue: 0.1634 time to fit residues: 87.9003 Evaluate side-chains 362 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 325 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 165 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN C 186 ASN G 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.050156 restraints weight = 85942.210| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.37 r_work: 0.2530 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21095 Z= 0.184 Angle : 0.730 9.956 28881 Z= 0.361 Chirality : 0.047 0.235 3521 Planarity : 0.005 0.070 3431 Dihedral : 8.103 77.271 5116 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 2.63 % Allowed : 10.44 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 0.96 % Twisted General : 0.13 % 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 are not related in a simple way. whole: 0.44 (0.17), residues: 2341 helix: 1.83 (0.28), residues: 387 sheet: 1.03 (0.19), residues: 703 loop : -0.65 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.018 0.002 TYR L 91 PHE 0.025 0.002 PHE C 383 TRP 0.041 0.002 TRP L 35 HIS 0.008 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00432 (20928) covalent geometry : angle 0.68496 (28422) SS BOND : bond 0.00604 ( 42) SS BOND : angle 1.76221 ( 84) hydrogen bonds : bond 0.06536 ( 530) hydrogen bonds : angle 5.10121 ( 1383) link_ALPHA1-2 : bond 0.01047 ( 7) link_ALPHA1-2 : angle 2.36331 ( 21) link_ALPHA1-3 : bond 0.00969 ( 11) link_ALPHA1-3 : angle 2.18536 ( 33) link_ALPHA1-6 : bond 0.00839 ( 7) link_ALPHA1-6 : angle 1.82397 ( 21) link_BETA1-4 : bond 0.00387 ( 45) link_BETA1-4 : angle 1.80238 ( 135) link_BETA1-6 : bond 0.01209 ( 3) link_BETA1-6 : angle 2.82336 ( 9) link_NAG-ASN : bond 0.00317 ( 52) link_NAG-ASN : angle 2.45581 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 328 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 34 LYS cc_start: 0.8759 (mppt) cc_final: 0.8388 (mppt) REVERT: H 100 SER cc_start: 0.8200 (p) cc_final: 0.7946 (p) REVERT: J 36 TRP cc_start: 0.7786 (m100) cc_final: 0.7440 (m100) REVERT: K 6 GLU cc_start: 0.7874 (mp0) cc_final: 0.7502 (mt-10) REVERT: K 57 ASP cc_start: 0.8629 (t0) cc_final: 0.8372 (t0) REVERT: L 51 ASP cc_start: 0.8225 (t0) cc_final: 0.7980 (t0) REVERT: L 53 GLU cc_start: 0.8747 (mp0) cc_final: 0.8412 (mp0) REVERT: A 80 ASN cc_start: 0.8679 (m-40) cc_final: 0.8351 (p0) REVERT: C 473 SER cc_start: 0.8285 (p) cc_final: 0.7850 (t) REVERT: C 504 ARG cc_start: 0.9064 (ttm-80) cc_final: 0.8803 (mtt180) REVERT: G 45 TRP cc_start: 0.7288 (p90) cc_final: 0.6509 (p90) REVERT: G 396 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8183 (m-80) outliers start: 55 outliers final: 45 residues processed: 355 average time/residue: 0.1643 time to fit residues: 87.4143 Evaluate side-chains 364 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 72 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 143 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 181 optimal weight: 0.0870 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.055187 restraints weight = 63797.925| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.92 r_work: 0.2555 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21095 Z= 0.182 Angle : 0.730 9.642 28881 Z= 0.361 Chirality : 0.047 0.336 3521 Planarity : 0.005 0.073 3431 Dihedral : 7.998 74.740 5116 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 2.25 % Allowed : 11.30 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 1.92 % Twisted General : 0.18 % 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 are not related in a simple way. whole: 0.34 (0.17), residues: 2341 helix: 1.82 (0.28), residues: 387 sheet: 0.98 (0.19), residues: 704 loop : -0.75 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 38 TYR 0.022 0.002 TYR F 52 PHE 0.023 0.002 PHE C 383 TRP 0.041 0.002 TRP L 35 HIS 0.007 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00427 (20928) covalent geometry : angle 0.68426 (28422) SS BOND : bond 0.00492 ( 42) SS BOND : angle 1.76837 ( 84) hydrogen bonds : bond 0.06451 ( 530) hydrogen bonds : angle 5.11954 ( 1383) link_ALPHA1-2 : bond 0.01042 ( 7) link_ALPHA1-2 : angle 2.36729 ( 21) link_ALPHA1-3 : bond 0.00977 ( 11) link_ALPHA1-3 : angle 2.08829 ( 33) link_ALPHA1-6 : bond 0.00843 ( 7) link_ALPHA1-6 : angle 1.79696 ( 21) link_BETA1-4 : bond 0.00388 ( 45) link_BETA1-4 : angle 1.78202 ( 135) link_BETA1-6 : bond 0.01199 ( 3) link_BETA1-6 : angle 2.82208 ( 9) link_NAG-ASN : bond 0.00305 ( 52) link_NAG-ASN : angle 2.52487 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 ARG cc_start: 0.8987 (tmm-80) cc_final: 0.8528 (ttp80) REVERT: F 34 LYS cc_start: 0.8833 (mppt) cc_final: 0.8478 (mppt) REVERT: H 100 SER cc_start: 0.8376 (p) cc_final: 0.8138 (p) REVERT: J 36 TRP cc_start: 0.7939 (m100) cc_final: 0.7605 (m100) REVERT: K 6 GLU cc_start: 0.7993 (mp0) cc_final: 0.7619 (mt-10) REVERT: L 35 TRP cc_start: 0.8077 (m100) cc_final: 0.7865 (m100) REVERT: L 53 GLU cc_start: 0.8880 (mp0) cc_final: 0.8549 (mp0) REVERT: A 80 ASN cc_start: 0.8826 (m-40) cc_final: 0.8413 (p0) REVERT: B 611 ASN cc_start: 0.8883 (t0) cc_final: 0.8647 (m-40) REVERT: C 473 SER cc_start: 0.8453 (p) cc_final: 0.8004 (t) REVERT: C 504 ARG cc_start: 0.9161 (ttm-80) cc_final: 0.8904 (mtt180) REVERT: G 45 TRP cc_start: 0.7329 (p90) cc_final: 0.6438 (p90) REVERT: G 325 ASP cc_start: 0.7966 (p0) cc_final: 0.7763 (p0) REVERT: G 396 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8256 (m-80) outliers start: 47 outliers final: 44 residues processed: 350 average time/residue: 0.1732 time to fit residues: 90.5090 Evaluate side-chains 372 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 327 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 174 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 HIS H 105 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.050222 restraints weight = 71075.245| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.04 r_work: 0.2537 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21095 Z= 0.190 Angle : 0.745 9.961 28881 Z= 0.369 Chirality : 0.048 0.459 3521 Planarity : 0.005 0.075 3431 Dihedral : 7.904 71.219 5116 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 2.49 % Allowed : 11.11 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 1.92 % Twisted General : 0.18 % 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 are not related in a simple way. whole: 0.23 (0.17), residues: 2341 helix: 1.76 (0.27), residues: 387 sheet: 0.87 (0.19), residues: 710 loop : -0.82 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 500 TYR 0.029 0.002 TYR F 52 PHE 0.025 0.002 PHE C 383 TRP 0.044 0.002 TRP L 35 HIS 0.007 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00446 (20928) covalent geometry : angle 0.70068 (28422) SS BOND : bond 0.00584 ( 42) SS BOND : angle 1.83209 ( 84) hydrogen bonds : bond 0.06627 ( 530) hydrogen bonds : angle 5.13274 ( 1383) link_ALPHA1-2 : bond 0.01001 ( 7) link_ALPHA1-2 : angle 2.32789 ( 21) link_ALPHA1-3 : bond 0.00948 ( 11) link_ALPHA1-3 : angle 2.07928 ( 33) link_ALPHA1-6 : bond 0.00866 ( 7) link_ALPHA1-6 : angle 1.78885 ( 21) link_BETA1-4 : bond 0.00388 ( 45) link_BETA1-4 : angle 1.80967 ( 135) link_BETA1-6 : bond 0.01180 ( 3) link_BETA1-6 : angle 2.84074 ( 9) link_NAG-ASN : bond 0.00319 ( 52) link_NAG-ASN : angle 2.45836 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4682 Ramachandran restraints generated. 2341 Oldfield, 0 Emsley, 2341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 34 LYS cc_start: 0.8845 (mppt) cc_final: 0.8498 (mppt) REVERT: H 100 SER cc_start: 0.8388 (p) cc_final: 0.8150 (p) REVERT: J 36 TRP cc_start: 0.7967 (m100) cc_final: 0.7602 (m100) REVERT: J 59 ILE cc_start: 0.8372 (mm) cc_final: 0.8127 (mm) REVERT: K 6 GLU cc_start: 0.7994 (mp0) cc_final: 0.7607 (mt-10) REVERT: L 53 GLU cc_start: 0.8878 (mp0) cc_final: 0.8558 (mp0) REVERT: A 80 ASN cc_start: 0.8840 (m-40) cc_final: 0.8409 (p0) REVERT: A 327 ARG cc_start: 0.9036 (mmm-85) cc_final: 0.8677 (mmt90) REVERT: C 473 SER cc_start: 0.8492 (p) cc_final: 0.8037 (t) REVERT: C 504 ARG cc_start: 0.9162 (ttm-80) cc_final: 0.8904 (mtt180) REVERT: G 45 TRP cc_start: 0.7445 (p90) cc_final: 0.6615 (p90) REVERT: G 207 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8627 (mmtt) REVERT: G 325 ASP cc_start: 0.7867 (p0) cc_final: 0.7657 (p0) REVERT: G 396 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8251 (m-80) outliers start: 52 outliers final: 44 residues processed: 351 average time/residue: 0.1656 time to fit residues: 87.3381 Evaluate side-chains 367 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 TRP Chi-restraints excluded: chain E residue 50 TRP Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 618 SER Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 632 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 378 CYS Chi-restraints excluded: chain G residue 396 TYR Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 29 optimal weight: 0.6980 chunk 168 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 151 optimal weight: 0.0970 chunk 102 optimal weight: 0.0030 chunk 50 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 105 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.066256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.052741 restraints weight = 69513.406| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.01 r_work: 0.2610 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21095 Z= 0.124 Angle : 0.649 9.139 28881 Z= 0.320 Chirality : 0.044 0.284 3521 Planarity : 0.004 0.068 3431 Dihedral : 7.217 66.742 5116 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 2.01 % Allowed : 11.87 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.04 % Twisted Proline : 1.92 % Twisted General : 0.18 % 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 are not related in a simple way. whole: 0.42 (0.17), residues: 2341 helix: 2.03 (0.28), residues: 387 sheet: 0.96 (0.19), residues: 718 loop : -0.72 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.018 0.001 TYR L 91 PHE 0.013 0.001 PHE A 53 TRP 0.061 0.001 TRP L 35 HIS 0.005 0.001 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00267 (20928) covalent geometry : angle 0.61113 (28422) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.36926 ( 84) hydrogen bonds : bond 0.04903 ( 530) hydrogen bonds : angle 4.83944 ( 1383) link_ALPHA1-2 : bond 0.00960 ( 7) link_ALPHA1-2 : angle 2.35992 ( 21) link_ALPHA1-3 : bond 0.01036 ( 11) link_ALPHA1-3 : angle 1.75649 ( 33) link_ALPHA1-6 : bond 0.00896 ( 7) link_ALPHA1-6 : angle 1.71375 ( 21) link_BETA1-4 : bond 0.00461 ( 45) link_BETA1-4 : angle 1.58924 ( 135) link_BETA1-6 : bond 0.01026 ( 3) link_BETA1-6 : angle 2.36757 ( 9) link_NAG-ASN : bond 0.00234 ( 52) link_NAG-ASN : angle 2.13831 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5580.35 seconds wall clock time: 96 minutes 40.25 seconds (5800.25 seconds total)