Starting phenix.real_space_refine on Wed Nov 19 03:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6crq_7568/11_2025/6crq_7568.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crq_7568/11_2025/6crq_7568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6crq_7568/11_2025/6crq_7568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crq_7568/11_2025/6crq_7568.map" model { file = "/net/cci-nas-00/data/ceres_data/6crq_7568/11_2025/6crq_7568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crq_7568/11_2025/6crq_7568.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 123 5.16 5 C 12702 2.51 5 N 3399 2.21 5 O 4047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20271 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3537 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "B" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3537 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "F" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3537 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 426} Chain breaks: 3 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 967 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "M" 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: "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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: "B" 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: 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: "F" 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: "H" 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 Time building chain proxies: 5.47, per 1000 atoms: 0.27 Number of scatterers: 20271 At special positions: 0 Unit cell: (146.88, 140.76, 119.34, 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 123 16.00 O 4047 8.00 N 3399 7.00 C 12702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.19 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.14 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.17 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.06 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.25 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.11 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.70 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.53 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS G 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.08 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.17 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.10 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.06 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.22 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.04 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS H 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=1.92 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA a 3 " - " MAN a 4 " " BMA m 3 " - " MAN m 4 " 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 O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 807 " - " ASN A 160 " " NAG A 818 " - " ASN A 234 " " NAG A 832 " - " ASN A 339 " " NAG B 807 " - " ASN B 160 " " NAG B 818 " - " ASN B 234 " " NAG B 832 " - " ASN B 339 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 611 " " NAG F 807 " - " ASN F 160 " " NAG F 818 " - " ASN F 234 " " NAG F 832 " - " ASN F 339 " " NAG G 701 " - " ASN G 637 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 611 " " NAG H 701 " - " ASN H 637 " " NAG H 702 " - " ASN H 618 " " NAG H 703 " - " ASN H 611 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 363 " " NAG S 1 " - " ASN A 197 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 301 " " NAG W 1 " - " ASN A 88 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN B 262 " " NAG Z 1 " - " ASN B 448 " " NAG a 1 " - " ASN B 276 " " NAG b 1 " - " ASN B 295 " " NAG c 1 " - " ASN B 386 " " NAG d 1 " - " ASN B 363 " " NAG e 1 " - " ASN B 197 " " NAG f 1 " - " ASN B 133 " " NAG g 1 " - " ASN B 156 " " NAG h 1 " - " ASN B 301 " " NAG i 1 " - " ASN B 88 " " NAG j 1 " - " ASN B 332 " " NAG k 1 " - " ASN F 262 " " NAG l 1 " - " ASN F 448 " " NAG m 1 " - " ASN F 276 " " NAG n 1 " - " ASN F 295 " " NAG o 1 " - " ASN F 386 " " NAG p 1 " - " ASN F 363 " " NAG q 1 " - " ASN F 197 " " NAG r 1 " - " ASN F 133 " " NAG s 1 " - " ASN F 156 " " NAG t 1 " - " ASN F 301 " " NAG u 1 " - " ASN F 88 " " NAG v 1 " - " ASN F 332 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 963.1 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.518A 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 335 through 354 removed outlier: 3.888A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 3.811A pdb=" N PHE A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 392' Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.844A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.527A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.576A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 543 Processing helix chain 'C' and resid 574 through 597 Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 626 removed outlier: 3.744A pdb=" N MET C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.534A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 Processing helix chain 'C' and resid 650 through 663 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 77 through 83 Proline residue: E 80 - end of helix Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.910A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.848A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.789A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.569A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 Processing helix chain 'G' and resid 529 through 534 removed outlier: 3.604A pdb=" N SER G 534 " --> pdb=" O MET G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 Processing helix chain 'G' and resid 574 through 596 Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.739A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 removed outlier: 3.741A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'I' and resid 25 through 32 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 27 through 31 No H-bonds generated for 'chain 'K' and resid 27 through 31' Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing helix chain 'F' and resid 57 through 64 removed outlier: 3.822A pdb=" N TYR F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.821A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.832A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.561A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 removed outlier: 3.823A pdb=" N SER H 534 " --> pdb=" O MET H 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 543 Processing helix chain 'H' and resid 574 through 597 Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 626 removed outlier: 3.693A pdb=" N MET H 626 " --> pdb=" O ILE H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 627 through 636 removed outlier: 4.083A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 650 removed outlier: 3.555A pdb=" N GLN H 650 " --> pdb=" O LEU H 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 663 Processing helix chain 'J' and resid 25 through 30 Processing helix chain 'J' and resid 60 through 66 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 499 removed outlier: 4.926A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.695A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.524A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.946A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.183A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.631A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 284 through 285 removed outlier: 6.271A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 308 removed outlier: 4.737A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.646A pdb=" N ILE D 35 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP D 50 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.606A pdb=" N CYS D 92 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.439A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.439A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.617A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 44 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 494 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 42 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N VAL B 496 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N TYR B 40 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL B 38 " --> pdb=" O PRO B 498 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL G 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL B 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR G 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N TYR B 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS G 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AC2, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AC4, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.116A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 6.300A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 274 removed outlier: 4.186A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 302 through 308 removed outlier: 4.705A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.684A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.636A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.068A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.068A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 496 through 499 removed outlier: 4.907A pdb=" N VAL F 36 " --> pdb=" O THR H 606 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.138A pdb=" N VAL F 44 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AD8, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'F' and resid 175 through 177 removed outlier: 4.001A pdb=" N THR F 132 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER F 158 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'F' and resid 200 through 203 removed outlier: 6.185A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.375A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 284 through 285 removed outlier: 6.160A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 302 through 308 removed outlier: 4.707A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.626A pdb=" N ILE J 35 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP J 50 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.692A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.690A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 11 through 12 749 hydrogen bonds defined for protein. 1902 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: 4.31 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: 5700 1.33 - 1.47: 5920 1.47 - 1.60: 8884 1.60 - 1.73: 1 1.73 - 1.86: 168 Bond restraints: 20673 Sorted by residual: bond pdb=" C ASN A 300 " pdb=" N ASN A 301 " ideal model delta sigma weight residual 1.333 1.435 -0.102 1.45e-02 4.76e+03 4.96e+01 bond pdb=" C ASN F 300 " pdb=" N ASN F 301 " ideal model delta sigma weight residual 1.333 1.435 -0.102 1.45e-02 4.76e+03 4.93e+01 bond pdb=" C GLU A 87 " pdb=" N ASN A 88 " ideal model delta sigma weight residual 1.333 1.251 0.082 1.39e-02 5.18e+03 3.51e+01 bond pdb=" CB LEU E 47 " pdb=" CG LEU E 47 " ideal model delta sigma weight residual 1.530 1.430 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " ideal model delta sigma weight residual 1.497 1.432 0.065 1.40e-02 5.10e+03 2.15e+01 ... (remaining 20668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 25510 2.46 - 4.92: 2141 4.92 - 7.37: 341 7.37 - 9.83: 37 9.83 - 12.29: 6 Bond angle restraints: 28035 Sorted by residual: angle pdb=" N VAL B 172 " pdb=" CA VAL B 172 " pdb=" C VAL B 172 " ideal model delta sigma weight residual 110.72 121.07 -10.35 1.01e+00 9.80e-01 1.05e+02 angle pdb=" C ARG B 298 " pdb=" N PRO B 299 " pdb=" CA PRO B 299 " ideal model delta sigma weight residual 120.31 130.04 -9.73 9.80e-01 1.04e+00 9.86e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 120.31 129.56 -9.25 9.80e-01 1.04e+00 8.91e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 120.31 129.54 -9.23 9.80e-01 1.04e+00 8.86e+01 angle pdb=" N ALA H 525 " pdb=" CA ALA H 525 " pdb=" C ALA H 525 " ideal model delta sigma weight residual 111.28 120.89 -9.61 1.09e+00 8.42e-01 7.78e+01 ... (remaining 28030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 13124 21.82 - 43.63: 374 43.63 - 65.45: 116 65.45 - 87.27: 68 87.27 - 109.08: 37 Dihedral angle restraints: 13719 sinusoidal: 6867 harmonic: 6852 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual 93.00 48.42 44.58 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.42 44.42 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS F 131 " pdb=" SG CYS F 131 " pdb=" SG CYS F 157 " pdb=" CB CYS F 157 " ideal model delta sinusoidal sigma weight residual 93.00 50.73 42.27 1 1.00e+01 1.00e-02 2.50e+01 ... (remaining 13716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3099 0.133 - 0.266: 299 0.266 - 0.399: 15 0.399 - 0.532: 12 0.532 - 0.665: 7 Chirality restraints: 3432 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.50e+01 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.69e+01 chirality pdb=" C1 NAG p 2 " pdb=" O4 NAG p 1 " pdb=" C2 NAG p 2 " pdb=" O5 NAG p 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.48e+01 ... (remaining 3429 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 611 " -0.147 2.00e-02 2.50e+03 1.54e-01 2.97e+02 pdb=" CG ASN H 611 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN H 611 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN H 611 " 0.241 2.00e-02 2.50e+03 pdb=" C1 NAG H 703 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 611 " -0.142 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN G 611 " 0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN G 611 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN G 611 " 0.235 2.00e-02 2.50e+03 pdb=" C1 NAG G 703 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.129 2.00e-02 2.50e+03 1.34e-01 2.25e+02 pdb=" CG ASN A 332 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.210 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.158 2.00e-02 2.50e+03 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 51 2.45 - 3.06: 13918 3.06 - 3.68: 27741 3.68 - 4.29: 44655 4.29 - 4.90: 70874 Nonbonded interactions: 157239 Sorted by model distance: nonbonded pdb=" C8 NAG r 1 " pdb=" O3 NAG r 1 " model vdw 1.839 3.460 nonbonded pdb=" O3 NAG m 2 " pdb=" O7 NAG m 2 " model vdw 1.865 3.040 nonbonded pdb=" O3 NAG A 807 " pdb=" O7 NAG A 807 " model vdw 1.866 3.040 nonbonded pdb=" C8 NAG f 1 " pdb=" O3 NAG f 1 " model vdw 1.867 3.460 nonbonded pdb=" O3 NAG F 807 " pdb=" O7 NAG F 807 " model vdw 1.868 3.040 ... (remaining 157234 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Y' selection = chain 'a' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'S' selection = chain 'e' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.680 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.017 0.668 20814 Z= 0.868 Angle : 1.557 15.703 28422 Z= 0.966 Chirality : 0.087 0.665 3432 Planarity : 0.007 0.076 3432 Dihedral : 14.008 109.081 9195 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 1.59 % Favored : 97.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: 1.77 (0.17), residues: 2343 helix: -0.15 (0.22), residues: 459 sheet: 1.14 (0.21), residues: 591 loop : 2.00 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 503 TYR 0.051 0.005 TYR A 173 PHE 0.021 0.004 PHE L 98 TRP 0.046 0.007 TRP G 610 HIS 0.008 0.002 HIS K 32 Details of bonding type rmsd covalent geometry : bond 0.01507 (20673) covalent geometry : angle 1.49750 (28035) SS BOND : bond 0.15698 ( 36) SS BOND : angle 4.00203 ( 72) hydrogen bonds : bond 0.19954 ( 720) hydrogen bonds : angle 7.54414 ( 1902) link_ALPHA1-3 : bond 0.03597 ( 3) link_ALPHA1-3 : angle 2.06541 ( 9) link_ALPHA1-6 : bond 0.04245 ( 3) link_ALPHA1-6 : angle 3.69472 ( 9) link_BETA1-4 : bond 0.03159 ( 45) link_BETA1-4 : angle 2.72656 ( 135) link_NAG-ASN : bond 0.05191 ( 54) link_NAG-ASN : angle 4.81401 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 732 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8828 (m-40) cc_final: 0.8015 (p0) REVERT: A 104 MET cc_start: 0.8541 (ttt) cc_final: 0.8220 (tpp) REVERT: A 207 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7334 (ptpt) REVERT: A 295 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6348 (t0) REVERT: A 348 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8447 (mm-40) REVERT: A 443 ILE cc_start: 0.8267 (mm) cc_final: 0.7847 (mm) REVERT: C 530 MET cc_start: 0.7554 (mtp) cc_final: 0.7113 (mtp) REVERT: C 618 ASN cc_start: 0.6334 (OUTLIER) cc_final: 0.6020 (m-40) REVERT: C 635 ILE cc_start: 0.8963 (pt) cc_final: 0.8673 (pt) REVERT: C 650 GLN cc_start: 0.5986 (tp40) cc_final: 0.5512 (tp40) REVERT: D 34 LEU cc_start: 0.9168 (mt) cc_final: 0.8749 (mp) REVERT: D 76 PHE cc_start: 0.8550 (m-80) cc_final: 0.8198 (m-10) REVERT: D 80 MET cc_start: 0.8823 (ttp) cc_final: 0.8574 (ttt) REVERT: E 6 GLN cc_start: 0.7046 (mt0) cc_final: 0.6697 (mt0) REVERT: E 23 CYS cc_start: 0.4025 (p) cc_final: 0.3412 (p) REVERT: B 38 VAL cc_start: 0.8835 (t) cc_final: 0.8588 (p) REVERT: B 97 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8124 (ttmt) REVERT: B 104 MET cc_start: 0.8596 (ttt) cc_final: 0.8143 (tpp) REVERT: B 348 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8683 (mm-40) REVERT: B 442 VAL cc_start: 0.7869 (t) cc_final: 0.7585 (p) REVERT: G 530 MET cc_start: 0.7777 (mtp) cc_final: 0.7490 (mtp) REVERT: I 32 THR cc_start: 0.8574 (m) cc_final: 0.8132 (p) REVERT: I 73 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7663 (mtp85) REVERT: K 42 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8214 (mp10) REVERT: K 102 THR cc_start: 0.7806 (p) cc_final: 0.7410 (p) REVERT: F 38 VAL cc_start: 0.8966 (t) cc_final: 0.8705 (t) REVERT: F 98 ASN cc_start: 0.8138 (t0) cc_final: 0.7523 (t0) REVERT: F 99 ASN cc_start: 0.8531 (m-40) cc_final: 0.8006 (p0) REVERT: F 100 MET cc_start: 0.7960 (mtp) cc_final: 0.7388 (ttm) REVERT: F 104 MET cc_start: 0.8512 (ttt) cc_final: 0.8117 (tpp) REVERT: F 178 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8178 (ttm-80) REVERT: F 194 ILE cc_start: 0.9089 (tt) cc_final: 0.8885 (tt) REVERT: F 328 GLN cc_start: 0.8464 (tt0) cc_final: 0.8062 (mp10) REVERT: F 442 VAL cc_start: 0.7536 (t) cc_final: 0.7211 (p) REVERT: F 474 ASP cc_start: 0.7139 (t0) cc_final: 0.6715 (p0) REVERT: H 530 MET cc_start: 0.7724 (mtp) cc_final: 0.7028 (mtp) REVERT: H 618 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6390 (m-40) REVERT: H 634 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7301 (tp30) REVERT: J 24 THR cc_start: 0.7555 (t) cc_final: 0.7313 (t) REVERT: J 25 SER cc_start: 0.8382 (t) cc_final: 0.7931 (p) REVERT: J 87 THR cc_start: 0.8650 (m) cc_final: 0.8275 (p) REVERT: L 30 TYR cc_start: 0.7574 (m-80) cc_final: 0.7157 (m-80) REVERT: L 102 THR cc_start: 0.7881 (p) cc_final: 0.7488 (t) outliers start: 22 outliers final: 4 residues processed: 746 average time/residue: 0.1719 time to fit residues: 187.3438 Evaluate side-chains 382 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 374 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 99 ASN A 302 ASN A 425 ASN A 440 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 6 GLN B 195 ASN B 425 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 625 ASN ** G 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 422 GLN F 425 ASN H 543 ASN H 625 ASN J 1 GLN J 6 GLN J 79 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083099 restraints weight = 55868.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085517 restraints weight = 33554.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.087205 restraints weight = 23986.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.088361 restraints weight = 19070.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.089164 restraints weight = 16263.560| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20814 Z= 0.207 Angle : 0.937 27.717 28422 Z= 0.441 Chirality : 0.052 0.500 3432 Planarity : 0.005 0.055 3432 Dihedral : 10.005 74.044 4734 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.34 % Allowed : 2.93 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: 1.33 (0.17), residues: 2343 helix: 0.82 (0.24), residues: 438 sheet: 0.65 (0.20), residues: 627 loop : 1.26 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.025 0.002 TYR A 173 PHE 0.028 0.002 PHE E 49 TRP 0.030 0.003 TRP A 479 HIS 0.004 0.001 HIS E 32 Details of bonding type rmsd covalent geometry : bond 0.00450 (20673) covalent geometry : angle 0.85260 (28035) SS BOND : bond 0.00590 ( 36) SS BOND : angle 1.68227 ( 72) hydrogen bonds : bond 0.05773 ( 720) hydrogen bonds : angle 5.90093 ( 1902) link_ALPHA1-3 : bond 0.01245 ( 3) link_ALPHA1-3 : angle 3.11887 ( 9) link_ALPHA1-6 : bond 0.02196 ( 3) link_ALPHA1-6 : angle 2.34213 ( 9) link_BETA1-4 : bond 0.00783 ( 45) link_BETA1-4 : angle 2.73044 ( 135) link_NAG-ASN : bond 0.00690 ( 54) link_NAG-ASN : angle 4.47957 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 488 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.7343 (mp) cc_final: 0.7088 (mm) REVERT: A 182 VAL cc_start: 0.8845 (t) cc_final: 0.8621 (p) REVERT: A 207 LYS cc_start: 0.7706 (mmmt) cc_final: 0.7352 (ptpt) REVERT: C 543 ASN cc_start: 0.8097 (t0) cc_final: 0.7847 (t0) REVERT: C 648 GLU cc_start: 0.8909 (pt0) cc_final: 0.8323 (pt0) REVERT: D 31 ARG cc_start: 0.8348 (tpp80) cc_final: 0.7648 (mtt-85) REVERT: D 73 ARG cc_start: 0.8499 (ptp-110) cc_final: 0.7999 (mtp85) REVERT: D 76 PHE cc_start: 0.8439 (m-80) cc_final: 0.8152 (m-10) REVERT: E 42 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8123 (mp10) REVERT: B 97 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8232 (ttpt) REVERT: B 103 GLN cc_start: 0.7459 (mt0) cc_final: 0.7143 (tm-30) REVERT: B 107 ASP cc_start: 0.8321 (m-30) cc_final: 0.6864 (m-30) REVERT: B 442 VAL cc_start: 0.7757 (t) cc_final: 0.7408 (p) REVERT: G 530 MET cc_start: 0.7299 (mtp) cc_final: 0.6916 (mmm) REVERT: G 621 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6674 (tm-30) REVERT: G 648 GLU cc_start: 0.8835 (pt0) cc_final: 0.8629 (pt0) REVERT: I 31 ARG cc_start: 0.8631 (ttm110) cc_final: 0.7960 (mtm-85) REVERT: I 100 TYR cc_start: 0.7770 (m-80) cc_final: 0.7550 (m-80) REVERT: K 42 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8145 (mp10) REVERT: K 66 GLN cc_start: 0.9021 (pm20) cc_final: 0.8592 (pp30) REVERT: K 86 TYR cc_start: 0.8686 (m-80) cc_final: 0.8476 (m-80) REVERT: F 99 ASN cc_start: 0.7915 (m-40) cc_final: 0.7291 (m-40) REVERT: F 103 GLN cc_start: 0.7472 (mp10) cc_final: 0.6744 (mp10) REVERT: F 104 MET cc_start: 0.8097 (ttt) cc_final: 0.7595 (tpp) REVERT: F 161 MET cc_start: 0.7298 (tpt) cc_final: 0.6719 (tpt) REVERT: F 195 ASN cc_start: 0.8581 (t0) cc_final: 0.8125 (t0) REVERT: F 328 GLN cc_start: 0.8518 (tt0) cc_final: 0.8015 (mp10) REVERT: F 341 THR cc_start: 0.9236 (p) cc_final: 0.8909 (t) REVERT: F 494 LEU cc_start: 0.8660 (mt) cc_final: 0.7602 (mt) REVERT: F 502 LYS cc_start: 0.6064 (tppt) cc_final: 0.4876 (tptt) REVERT: H 530 MET cc_start: 0.7219 (mtp) cc_final: 0.6465 (mmm) REVERT: H 620 SER cc_start: 0.8563 (p) cc_final: 0.8307 (p) REVERT: H 621 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7301 (tm-30) REVERT: H 645 LEU cc_start: 0.9012 (mt) cc_final: 0.8777 (mt) REVERT: H 648 GLU cc_start: 0.8621 (pt0) cc_final: 0.8125 (pt0) REVERT: J 87 THR cc_start: 0.8829 (m) cc_final: 0.8434 (p) REVERT: J 102 LEU cc_start: 0.8230 (mp) cc_final: 0.7992 (mp) REVERT: L 30 TYR cc_start: 0.7683 (m-80) cc_final: 0.7227 (m-80) REVERT: L 86 TYR cc_start: 0.8834 (m-80) cc_final: 0.8505 (m-80) REVERT: L 96 GLU cc_start: 0.8292 (pt0) cc_final: 0.7907 (pt0) REVERT: L 102 THR cc_start: 0.7869 (p) cc_final: 0.7602 (p) outliers start: 7 outliers final: 3 residues processed: 495 average time/residue: 0.1520 time to fit residues: 114.5144 Evaluate side-chains 327 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 176 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN G 540 GLN G 607 ASN G 650 GLN F 170 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 ASN H 540 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077655 restraints weight = 56914.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079926 restraints weight = 34612.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081450 restraints weight = 25058.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.082511 restraints weight = 20271.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083212 restraints weight = 17490.403| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20814 Z= 0.265 Angle : 0.917 20.175 28422 Z= 0.439 Chirality : 0.053 0.429 3432 Planarity : 0.006 0.059 3432 Dihedral : 8.254 58.796 4734 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.14 % Allowed : 3.70 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: 0.55 (0.17), residues: 2343 helix: 0.74 (0.24), residues: 438 sheet: 0.63 (0.20), residues: 627 loop : 0.22 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 94 TYR 0.039 0.003 TYR D 100E PHE 0.021 0.002 PHE B 176 TRP 0.023 0.003 TRP G 610 HIS 0.008 0.002 HIS F 66 Details of bonding type rmsd covalent geometry : bond 0.00584 (20673) covalent geometry : angle 0.85824 (28035) SS BOND : bond 0.00715 ( 36) SS BOND : angle 1.69366 ( 72) hydrogen bonds : bond 0.05549 ( 720) hydrogen bonds : angle 5.70679 ( 1902) link_ALPHA1-3 : bond 0.02285 ( 3) link_ALPHA1-3 : angle 1.61434 ( 9) link_ALPHA1-6 : bond 0.01479 ( 3) link_ALPHA1-6 : angle 1.56273 ( 9) link_BETA1-4 : bond 0.00842 ( 45) link_BETA1-4 : angle 2.46377 ( 135) link_NAG-ASN : bond 0.00994 ( 54) link_NAG-ASN : angle 3.66399 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 425 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.7366 (mp) cc_final: 0.7010 (mm) REVERT: A 104 MET cc_start: 0.8140 (ttt) cc_final: 0.7931 (tpp) REVERT: A 182 VAL cc_start: 0.8998 (t) cc_final: 0.8778 (p) REVERT: A 207 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7457 (mtpt) REVERT: C 645 LEU cc_start: 0.8729 (mt) cc_final: 0.8506 (mt) REVERT: C 648 GLU cc_start: 0.8875 (pt0) cc_final: 0.8318 (pt0) REVERT: C 655 LYS cc_start: 0.7697 (mttm) cc_final: 0.7350 (mttm) REVERT: D 25 SER cc_start: 0.7897 (m) cc_final: 0.7554 (p) REVERT: D 34 LEU cc_start: 0.8887 (mt) cc_final: 0.8391 (mp) REVERT: E 42 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8165 (mp10) REVERT: B 97 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8465 (mtmt) REVERT: B 107 ASP cc_start: 0.8432 (m-30) cc_final: 0.8053 (t0) REVERT: B 494 LEU cc_start: 0.8445 (mm) cc_final: 0.7634 (mm) REVERT: G 530 MET cc_start: 0.7305 (mtp) cc_final: 0.7026 (mmm) REVERT: G 542 ARG cc_start: 0.5645 (ttt-90) cc_final: 0.5250 (ttp-110) REVERT: G 620 SER cc_start: 0.8347 (p) cc_final: 0.8131 (p) REVERT: G 621 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6684 (tm-30) REVERT: G 648 GLU cc_start: 0.8853 (pt0) cc_final: 0.8489 (pt0) REVERT: G 650 GLN cc_start: 0.6557 (tp40) cc_final: 0.5668 (tp-100) REVERT: I 31 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8066 (mtm-85) REVERT: I 48 ILE cc_start: 0.9617 (mm) cc_final: 0.9390 (mp) REVERT: I 86 ASP cc_start: 0.8337 (m-30) cc_final: 0.8116 (m-30) REVERT: K 42 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7962 (mp10) REVERT: K 86 TYR cc_start: 0.8880 (m-80) cc_final: 0.8445 (m-10) REVERT: F 100 MET cc_start: 0.7691 (mtp) cc_final: 0.7360 (ttm) REVERT: F 104 MET cc_start: 0.8349 (ttt) cc_final: 0.8139 (tpp) REVERT: F 195 ASN cc_start: 0.8542 (t0) cc_final: 0.8041 (t0) REVERT: F 328 GLN cc_start: 0.8743 (tt0) cc_final: 0.8148 (mp10) REVERT: H 530 MET cc_start: 0.7521 (mtp) cc_final: 0.6669 (mmm) REVERT: H 589 ASP cc_start: 0.8619 (t0) cc_final: 0.8283 (t0) REVERT: H 634 GLU cc_start: 0.6748 (tp30) cc_final: 0.6494 (tp30) REVERT: H 648 GLU cc_start: 0.8744 (pt0) cc_final: 0.8423 (pt0) REVERT: J 25 SER cc_start: 0.8623 (p) cc_final: 0.8417 (m) REVERT: J 30 GLU cc_start: 0.8066 (tp30) cc_final: 0.7822 (tp30) REVERT: L 12 SER cc_start: 0.6871 (t) cc_final: 0.5964 (m) REVERT: L 30 TYR cc_start: 0.7561 (m-80) cc_final: 0.7317 (m-80) REVERT: L 42 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8242 (mp10) REVERT: L 58 ILE cc_start: 0.7591 (mm) cc_final: 0.7387 (mt) REVERT: L 86 TYR cc_start: 0.8953 (m-80) cc_final: 0.8548 (m-80) REVERT: L 102 THR cc_start: 0.7939 (p) cc_final: 0.7596 (p) outliers start: 3 outliers final: 2 residues processed: 427 average time/residue: 0.1482 time to fit residues: 97.8005 Evaluate side-chains 309 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 85 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 225 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 HIS ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 GLN I 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078560 restraints weight = 56891.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080854 restraints weight = 34632.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082367 restraints weight = 24973.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083444 restraints weight = 20276.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084161 restraints weight = 17454.222| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20814 Z= 0.173 Angle : 0.800 17.942 28422 Z= 0.376 Chirality : 0.049 0.405 3432 Planarity : 0.005 0.092 3432 Dihedral : 7.533 58.598 4734 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.10 % Allowed : 1.92 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: 0.57 (0.17), residues: 2343 helix: 1.12 (0.26), residues: 405 sheet: 0.53 (0.20), residues: 630 loop : 0.17 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 94 TYR 0.031 0.002 TYR D 100E PHE 0.018 0.002 PHE I 76 TRP 0.026 0.002 TRP G 610 HIS 0.004 0.001 HIS I 79 Details of bonding type rmsd covalent geometry : bond 0.00377 (20673) covalent geometry : angle 0.73667 (28035) SS BOND : bond 0.00541 ( 36) SS BOND : angle 1.43745 ( 72) hydrogen bonds : bond 0.04527 ( 720) hydrogen bonds : angle 5.34449 ( 1902) link_ALPHA1-3 : bond 0.01499 ( 3) link_ALPHA1-3 : angle 2.37632 ( 9) link_ALPHA1-6 : bond 0.01124 ( 3) link_ALPHA1-6 : angle 1.70205 ( 9) link_BETA1-4 : bond 0.00581 ( 45) link_BETA1-4 : angle 2.25274 ( 135) link_NAG-ASN : bond 0.00600 ( 54) link_NAG-ASN : angle 3.56780 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7490 (mtpt) REVERT: C 530 MET cc_start: 0.7443 (mmm) cc_final: 0.6905 (mmm) REVERT: C 536 THR cc_start: 0.8707 (m) cc_final: 0.8445 (m) REVERT: C 543 ASN cc_start: 0.8010 (t0) cc_final: 0.7721 (t0) REVERT: C 548 ILE cc_start: 0.3459 (tp) cc_final: 0.3208 (tp) REVERT: C 648 GLU cc_start: 0.8800 (pt0) cc_final: 0.8592 (pt0) REVERT: D 25 SER cc_start: 0.7713 (m) cc_final: 0.7450 (p) REVERT: D 31 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7551 (mtt-85) REVERT: D 80 MET cc_start: 0.8231 (ttm) cc_final: 0.7767 (ttm) REVERT: B 97 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8434 (mtmt) REVERT: G 530 MET cc_start: 0.7412 (mtp) cc_final: 0.7086 (mmm) REVERT: G 542 ARG cc_start: 0.5435 (ttt-90) cc_final: 0.5172 (ttp-110) REVERT: G 589 ASP cc_start: 0.8368 (t0) cc_final: 0.8092 (t0) REVERT: G 621 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6859 (tm-30) REVERT: G 650 GLN cc_start: 0.6500 (tp40) cc_final: 0.5498 (tp-100) REVERT: I 31 ARG cc_start: 0.8505 (ttm110) cc_final: 0.8097 (mtp-110) REVERT: I 82 ILE cc_start: 0.9015 (mm) cc_final: 0.8781 (mm) REVERT: K 42 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7973 (mp10) REVERT: K 86 TYR cc_start: 0.8853 (m-80) cc_final: 0.8378 (m-10) REVERT: F 104 MET cc_start: 0.8370 (ttt) cc_final: 0.7964 (tpp) REVERT: F 195 ASN cc_start: 0.8484 (t0) cc_final: 0.7947 (t0) REVERT: F 328 GLN cc_start: 0.8710 (tt0) cc_final: 0.8105 (mp10) REVERT: H 530 MET cc_start: 0.7182 (mtp) cc_final: 0.6443 (mmm) REVERT: H 589 ASP cc_start: 0.8531 (t0) cc_final: 0.8216 (t0) REVERT: H 606 THR cc_start: 0.8687 (p) cc_final: 0.8073 (p) REVERT: H 626 MET cc_start: 0.7082 (tmm) cc_final: 0.5123 (tmm) REVERT: H 634 GLU cc_start: 0.6713 (tp30) cc_final: 0.6378 (tp30) REVERT: J 86 ASP cc_start: 0.8310 (m-30) cc_final: 0.7918 (m-30) REVERT: J 87 THR cc_start: 0.8915 (m) cc_final: 0.8522 (p) REVERT: L 30 TYR cc_start: 0.7576 (m-80) cc_final: 0.7316 (m-80) REVERT: L 86 TYR cc_start: 0.8901 (m-80) cc_final: 0.8433 (m-80) REVERT: L 102 THR cc_start: 0.8141 (p) cc_final: 0.7681 (p) outliers start: 2 outliers final: 0 residues processed: 401 average time/residue: 0.1380 time to fit residues: 87.3983 Evaluate side-chains 303 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 28 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 221 optimal weight: 0.0070 chunk 66 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN I 57 ASN J 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077709 restraints weight = 56991.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079969 restraints weight = 34510.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081497 restraints weight = 24899.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.082550 restraints weight = 20069.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083172 restraints weight = 17342.479| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20814 Z= 0.180 Angle : 0.774 16.590 28422 Z= 0.367 Chirality : 0.048 0.386 3432 Planarity : 0.005 0.076 3432 Dihedral : 7.526 59.978 4734 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 0.19 % Allowed : 2.59 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: 0.34 (0.17), residues: 2343 helix: 0.86 (0.25), residues: 423 sheet: 0.50 (0.20), residues: 645 loop : -0.05 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 94 TYR 0.025 0.002 TYR D 100E PHE 0.014 0.002 PHE B 176 TRP 0.051 0.002 TRP G 610 HIS 0.003 0.001 HIS J 79 Details of bonding type rmsd covalent geometry : bond 0.00397 (20673) covalent geometry : angle 0.71443 (28035) SS BOND : bond 0.00532 ( 36) SS BOND : angle 1.57334 ( 72) hydrogen bonds : bond 0.04469 ( 720) hydrogen bonds : angle 5.32358 ( 1902) link_ALPHA1-3 : bond 0.01804 ( 3) link_ALPHA1-3 : angle 1.89654 ( 9) link_ALPHA1-6 : bond 0.00961 ( 3) link_ALPHA1-6 : angle 1.70540 ( 9) link_BETA1-4 : bond 0.00599 ( 45) link_BETA1-4 : angle 2.15074 ( 135) link_NAG-ASN : bond 0.00525 ( 54) link_NAG-ASN : angle 3.37077 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8248 (tpp) cc_final: 0.7871 (tpp) REVERT: A 195 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8113 (t0) REVERT: A 207 LYS cc_start: 0.7766 (mmmt) cc_final: 0.7517 (mtpt) REVERT: C 536 THR cc_start: 0.8573 (m) cc_final: 0.8191 (m) REVERT: C 650 GLN cc_start: 0.7028 (tp40) cc_final: 0.6767 (mm110) REVERT: D 31 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7598 (mtt-85) REVERT: D 80 MET cc_start: 0.8233 (ttm) cc_final: 0.7842 (ttm) REVERT: E 42 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8226 (mp10) REVERT: B 35 TRP cc_start: 0.7495 (m-90) cc_final: 0.7206 (m-90) REVERT: B 97 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8482 (mtmt) REVERT: G 530 MET cc_start: 0.7605 (mtp) cc_final: 0.7245 (mmm) REVERT: G 538 THR cc_start: 0.9006 (t) cc_final: 0.8683 (m) REVERT: G 542 ARG cc_start: 0.5469 (ttt-90) cc_final: 0.5201 (ttp-110) REVERT: G 621 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6818 (tm-30) REVERT: G 650 GLN cc_start: 0.6827 (tp40) cc_final: 0.5660 (tp40) REVERT: I 6 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: I 31 ARG cc_start: 0.8545 (ttm110) cc_final: 0.8130 (mtp-110) REVERT: I 77 THR cc_start: 0.8785 (p) cc_final: 0.8547 (m) REVERT: I 107 THR cc_start: 0.9176 (t) cc_final: 0.8886 (p) REVERT: K 42 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7929 (mp10) REVERT: K 86 TYR cc_start: 0.8883 (m-80) cc_final: 0.8426 (m-10) REVERT: F 39 TYR cc_start: 0.7671 (m-80) cc_final: 0.7418 (m-80) REVERT: F 100 MET cc_start: 0.7828 (mtp) cc_final: 0.7497 (ttm) REVERT: F 104 MET cc_start: 0.8476 (ttt) cc_final: 0.8089 (tpp) REVERT: F 195 ASN cc_start: 0.8437 (t0) cc_final: 0.7895 (t0) REVERT: H 539 VAL cc_start: 0.8235 (t) cc_final: 0.7969 (t) REVERT: H 542 ARG cc_start: 0.5700 (ttt-90) cc_final: 0.5376 (ttp-110) REVERT: H 589 ASP cc_start: 0.8405 (t0) cc_final: 0.8075 (t0) REVERT: H 626 MET cc_start: 0.7063 (tmm) cc_final: 0.5917 (tmm) REVERT: J 9 SER cc_start: 0.8585 (p) cc_final: 0.8368 (m) REVERT: J 82 LEU cc_start: 0.8749 (mm) cc_final: 0.8533 (mm) REVERT: J 86 ASP cc_start: 0.8360 (m-30) cc_final: 0.7927 (m-30) REVERT: L 18 THR cc_start: 0.6246 (m) cc_final: 0.5774 (t) REVERT: L 30 TYR cc_start: 0.7584 (m-80) cc_final: 0.7355 (m-80) REVERT: L 42 GLN cc_start: 0.8633 (mp10) cc_final: 0.8144 (mp10) REVERT: L 86 TYR cc_start: 0.8887 (m-80) cc_final: 0.8364 (m-80) REVERT: L 102 THR cc_start: 0.8290 (p) cc_final: 0.7831 (p) outliers start: 4 outliers final: 2 residues processed: 391 average time/residue: 0.1375 time to fit residues: 84.9883 Evaluate side-chains 296 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 164 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN H 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077590 restraints weight = 56475.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.079831 restraints weight = 34424.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.081398 restraints weight = 24861.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.082449 restraints weight = 19957.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082982 restraints weight = 17245.255| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20814 Z= 0.181 Angle : 0.769 16.001 28422 Z= 0.368 Chirality : 0.048 0.389 3432 Planarity : 0.004 0.053 3432 Dihedral : 7.630 59.811 4734 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: 0.17 (0.17), residues: 2343 helix: 0.95 (0.26), residues: 405 sheet: 0.45 (0.20), residues: 645 loop : -0.26 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 77 TYR 0.028 0.002 TYR D 100E PHE 0.016 0.002 PHE J 76 TRP 0.056 0.002 TRP G 610 HIS 0.004 0.001 HIS I 35A Details of bonding type rmsd covalent geometry : bond 0.00403 (20673) covalent geometry : angle 0.71162 (28035) SS BOND : bond 0.00589 ( 36) SS BOND : angle 1.56482 ( 72) hydrogen bonds : bond 0.04333 ( 720) hydrogen bonds : angle 5.37349 ( 1902) link_ALPHA1-3 : bond 0.01815 ( 3) link_ALPHA1-3 : angle 2.00005 ( 9) link_ALPHA1-6 : bond 0.00837 ( 3) link_ALPHA1-6 : angle 1.54936 ( 9) link_BETA1-4 : bond 0.00569 ( 45) link_BETA1-4 : angle 2.13233 ( 135) link_NAG-ASN : bond 0.00546 ( 54) link_NAG-ASN : angle 3.29595 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8427 (ttt) cc_final: 0.8090 (tpp) REVERT: C 536 THR cc_start: 0.8515 (m) cc_final: 0.8139 (m) REVERT: C 543 ASN cc_start: 0.8103 (t0) cc_final: 0.7849 (t0) REVERT: C 650 GLN cc_start: 0.6906 (tp40) cc_final: 0.6624 (mm110) REVERT: D 9 SER cc_start: 0.8714 (m) cc_final: 0.8479 (m) REVERT: D 31 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7641 (mtt-85) REVERT: E 42 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8224 (mp10) REVERT: E 77 ARG cc_start: 0.7312 (ttp-110) cc_final: 0.7028 (ttp80) REVERT: B 97 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8538 (mtmt) REVERT: G 538 THR cc_start: 0.9049 (t) cc_final: 0.8759 (m) REVERT: G 542 ARG cc_start: 0.5469 (ttt-90) cc_final: 0.5102 (ttp-110) REVERT: G 621 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7222 (tm-30) REVERT: G 648 GLU cc_start: 0.8375 (pm20) cc_final: 0.7659 (pm20) REVERT: G 650 GLN cc_start: 0.6786 (tp40) cc_final: 0.5645 (tp40) REVERT: I 31 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8004 (mtp-110) REVERT: I 75 LEU cc_start: 0.8966 (mm) cc_final: 0.8656 (mt) REVERT: I 107 THR cc_start: 0.9177 (t) cc_final: 0.8883 (m) REVERT: K 42 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7921 (mp10) REVERT: K 46 LEU cc_start: 0.8495 (tp) cc_final: 0.8247 (tt) REVERT: K 71 TYR cc_start: 0.5472 (t80) cc_final: 0.5250 (t80) REVERT: K 86 TYR cc_start: 0.8870 (m-80) cc_final: 0.8370 (m-10) REVERT: F 39 TYR cc_start: 0.7731 (m-80) cc_final: 0.7522 (m-80) REVERT: F 100 MET cc_start: 0.7833 (mtp) cc_final: 0.7534 (ttm) REVERT: F 104 MET cc_start: 0.8376 (ttt) cc_final: 0.8136 (tpp) REVERT: H 542 ARG cc_start: 0.5722 (ttt-90) cc_final: 0.5359 (ttp-110) REVERT: H 589 ASP cc_start: 0.8431 (t0) cc_final: 0.8044 (t0) REVERT: H 626 MET cc_start: 0.7076 (tmm) cc_final: 0.6451 (tmm) REVERT: J 82 LEU cc_start: 0.8761 (mm) cc_final: 0.8541 (mm) REVERT: J 86 ASP cc_start: 0.8385 (m-30) cc_final: 0.7933 (m-30) REVERT: L 30 TYR cc_start: 0.7596 (m-80) cc_final: 0.7378 (m-80) REVERT: L 42 GLN cc_start: 0.8747 (mp10) cc_final: 0.8217 (mp10) REVERT: L 102 THR cc_start: 0.8400 (p) cc_final: 0.8182 (p) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1398 time to fit residues: 81.9082 Evaluate side-chains 292 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 207 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN C 607 ASN D 6 GLN B 216 HIS B 425 ASN I 6 GLN H 650 GLN H 653 GLN J 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.094160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076525 restraints weight = 57900.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078683 restraints weight = 35679.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080221 restraints weight = 25974.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081219 restraints weight = 20937.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.081910 restraints weight = 18123.861| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20814 Z= 0.217 Angle : 0.806 15.486 28422 Z= 0.385 Chirality : 0.049 0.381 3432 Planarity : 0.005 0.047 3432 Dihedral : 7.896 59.807 4734 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 0.14 % Allowed : 2.02 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: -0.11 (0.17), residues: 2343 helix: 0.78 (0.25), residues: 405 sheet: 0.21 (0.21), residues: 627 loop : -0.43 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 298 TYR 0.036 0.002 TYR D 100E PHE 0.018 0.002 PHE L 49 TRP 0.051 0.002 TRP G 610 HIS 0.005 0.002 HIS I 35A Details of bonding type rmsd covalent geometry : bond 0.00485 (20673) covalent geometry : angle 0.74804 (28035) SS BOND : bond 0.00629 ( 36) SS BOND : angle 1.67556 ( 72) hydrogen bonds : bond 0.04524 ( 720) hydrogen bonds : angle 5.46517 ( 1902) link_ALPHA1-3 : bond 0.01915 ( 3) link_ALPHA1-3 : angle 1.80433 ( 9) link_ALPHA1-6 : bond 0.00859 ( 3) link_ALPHA1-6 : angle 1.45464 ( 9) link_BETA1-4 : bond 0.00606 ( 45) link_BETA1-4 : angle 2.17681 ( 135) link_NAG-ASN : bond 0.00637 ( 54) link_NAG-ASN : angle 3.41254 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 358 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8470 (ttt) cc_final: 0.8136 (tpp) REVERT: A 217 TYR cc_start: 0.8317 (m-80) cc_final: 0.7018 (m-80) REVERT: C 530 MET cc_start: 0.7338 (mmm) cc_final: 0.6889 (mmm) REVERT: C 536 THR cc_start: 0.8578 (m) cc_final: 0.8319 (m) REVERT: C 543 ASN cc_start: 0.8159 (t0) cc_final: 0.7949 (t0) REVERT: C 626 MET cc_start: 0.6634 (tmm) cc_final: 0.6345 (tmm) REVERT: C 650 GLN cc_start: 0.6765 (tp40) cc_final: 0.6396 (mm110) REVERT: C 655 LYS cc_start: 0.7665 (mttm) cc_final: 0.7176 (mttp) REVERT: D 6 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: D 24 THR cc_start: 0.7822 (p) cc_final: 0.6629 (p) REVERT: D 31 ARG cc_start: 0.8302 (tpp80) cc_final: 0.7566 (mtt-85) REVERT: D 80 MET cc_start: 0.8091 (ttm) cc_final: 0.7607 (ttm) REVERT: D 107 THR cc_start: 0.9115 (t) cc_final: 0.8721 (p) REVERT: E 42 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8207 (mp10) REVERT: G 530 MET cc_start: 0.6792 (mmm) cc_final: 0.6352 (mmm) REVERT: G 542 ARG cc_start: 0.5713 (ttt-90) cc_final: 0.5217 (ttp-110) REVERT: G 650 GLN cc_start: 0.6833 (tp40) cc_final: 0.5685 (tp40) REVERT: I 6 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: I 31 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8053 (mtp-110) REVERT: I 75 LEU cc_start: 0.8839 (mm) cc_final: 0.8586 (mt) REVERT: I 100 TYR cc_start: 0.7727 (m-80) cc_final: 0.7283 (m-80) REVERT: I 102 LEU cc_start: 0.8536 (mt) cc_final: 0.8330 (mt) REVERT: I 107 THR cc_start: 0.9220 (t) cc_final: 0.8866 (p) REVERT: K 42 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7875 (mp10) REVERT: K 71 TYR cc_start: 0.5496 (t80) cc_final: 0.5082 (t80) REVERT: K 86 TYR cc_start: 0.8903 (m-80) cc_final: 0.8435 (m-10) REVERT: F 39 TYR cc_start: 0.7832 (m-80) cc_final: 0.7613 (m-80) REVERT: F 104 MET cc_start: 0.8577 (ttt) cc_final: 0.8283 (tpp) REVERT: H 542 ARG cc_start: 0.5738 (ttt-90) cc_final: 0.5255 (ttp-110) REVERT: H 626 MET cc_start: 0.7291 (tmm) cc_final: 0.6746 (tmm) REVERT: J 25 SER cc_start: 0.8290 (m) cc_final: 0.8068 (p) REVERT: J 82 LEU cc_start: 0.8780 (mm) cc_final: 0.8517 (mm) REVERT: J 86 ASP cc_start: 0.8395 (m-30) cc_final: 0.7993 (m-30) REVERT: J 87 THR cc_start: 0.9059 (m) cc_final: 0.8793 (t) REVERT: L 30 TYR cc_start: 0.7594 (m-80) cc_final: 0.7343 (m-80) REVERT: L 42 GLN cc_start: 0.8743 (mp10) cc_final: 0.8195 (mp10) REVERT: L 102 THR cc_start: 0.8482 (p) cc_final: 0.8119 (p) outliers start: 3 outliers final: 0 residues processed: 361 average time/residue: 0.1333 time to fit residues: 77.2351 Evaluate side-chains 293 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 123 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 216 optimal weight: 0.2980 chunk 162 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN H 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076573 restraints weight = 57800.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078755 restraints weight = 35638.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080292 restraints weight = 25914.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081166 restraints weight = 20881.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.081921 restraints weight = 18184.179| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20814 Z= 0.202 Angle : 0.794 15.122 28422 Z= 0.380 Chirality : 0.049 0.382 3432 Planarity : 0.005 0.056 3432 Dihedral : 7.946 59.980 4734 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: -0.28 (0.17), residues: 2343 helix: 0.51 (0.25), residues: 423 sheet: 0.22 (0.21), residues: 621 loop : -0.58 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 94 TYR 0.036 0.002 TYR D 100E PHE 0.023 0.002 PHE I 76 TRP 0.049 0.002 TRP B 69 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00456 (20673) covalent geometry : angle 0.73910 (28035) SS BOND : bond 0.00599 ( 36) SS BOND : angle 1.61623 ( 72) hydrogen bonds : bond 0.04493 ( 720) hydrogen bonds : angle 5.52057 ( 1902) link_ALPHA1-3 : bond 0.01801 ( 3) link_ALPHA1-3 : angle 1.90985 ( 9) link_ALPHA1-6 : bond 0.00810 ( 3) link_ALPHA1-6 : angle 1.40880 ( 9) link_BETA1-4 : bond 0.00616 ( 45) link_BETA1-4 : angle 2.13894 ( 135) link_NAG-ASN : bond 0.00559 ( 54) link_NAG-ASN : angle 3.28819 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8567 (ttt) cc_final: 0.8195 (tpp) REVERT: A 217 TYR cc_start: 0.8339 (m-80) cc_final: 0.7056 (m-80) REVERT: C 530 MET cc_start: 0.7561 (mmm) cc_final: 0.7217 (mmm) REVERT: C 536 THR cc_start: 0.8628 (m) cc_final: 0.8387 (m) REVERT: C 626 MET cc_start: 0.6829 (tmm) cc_final: 0.6481 (tmm) REVERT: C 648 GLU cc_start: 0.8731 (pt0) cc_final: 0.8524 (pt0) REVERT: C 650 GLN cc_start: 0.6660 (tp40) cc_final: 0.6446 (mm110) REVERT: D 52 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8239 (mttt) REVERT: D 80 MET cc_start: 0.8017 (ttm) cc_final: 0.7554 (ttm) REVERT: D 100 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7859 (mp10) REVERT: E 42 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8225 (mp10) REVERT: E 77 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.6919 (ttp80) REVERT: G 530 MET cc_start: 0.6955 (mmm) cc_final: 0.6729 (mmm) REVERT: G 542 ARG cc_start: 0.5607 (ttt-90) cc_final: 0.5305 (ttp-110) REVERT: G 650 GLN cc_start: 0.6683 (tp40) cc_final: 0.5530 (tp40) REVERT: I 31 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8062 (mtp-110) REVERT: I 75 LEU cc_start: 0.8807 (mm) cc_final: 0.8527 (mt) REVERT: I 102 LEU cc_start: 0.8519 (mt) cc_final: 0.8312 (mt) REVERT: I 107 THR cc_start: 0.9213 (t) cc_final: 0.8934 (m) REVERT: K 42 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7960 (mp10) REVERT: K 71 TYR cc_start: 0.5459 (t80) cc_final: 0.4737 (t80) REVERT: K 86 TYR cc_start: 0.8886 (m-80) cc_final: 0.8407 (m-10) REVERT: F 104 MET cc_start: 0.8580 (ttt) cc_final: 0.8307 (tpp) REVERT: H 542 ARG cc_start: 0.5668 (ttt-90) cc_final: 0.5304 (ttp-110) REVERT: H 590 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7849 (mt0) REVERT: H 626 MET cc_start: 0.7345 (tmm) cc_final: 0.6778 (tmm) REVERT: H 645 LEU cc_start: 0.8597 (mt) cc_final: 0.8352 (pp) REVERT: H 650 GLN cc_start: 0.6798 (tp40) cc_final: 0.5338 (tp-100) REVERT: J 82 LEU cc_start: 0.8748 (mm) cc_final: 0.8525 (mm) REVERT: J 87 THR cc_start: 0.9052 (m) cc_final: 0.8778 (t) REVERT: L 30 TYR cc_start: 0.7602 (m-80) cc_final: 0.7361 (m-80) REVERT: L 42 GLN cc_start: 0.8726 (mp10) cc_final: 0.8238 (mp10) REVERT: L 102 THR cc_start: 0.8585 (p) cc_final: 0.8293 (p) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.1374 time to fit residues: 79.2585 Evaluate side-chains 282 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 94 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.095134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077737 restraints weight = 57207.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.079948 restraints weight = 34960.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081432 restraints weight = 25303.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.082300 restraints weight = 20485.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083110 restraints weight = 17850.286| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20814 Z= 0.156 Angle : 0.756 14.517 28422 Z= 0.363 Chirality : 0.048 0.390 3432 Planarity : 0.004 0.050 3432 Dihedral : 7.721 59.627 4734 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 0.10 % Allowed : 0.72 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: -0.11 (0.17), residues: 2343 helix: 0.73 (0.25), residues: 423 sheet: 0.36 (0.20), residues: 669 loop : -0.55 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 94 TYR 0.028 0.001 TYR B 173 PHE 0.027 0.002 PHE I 97 TRP 0.028 0.002 TRP B 69 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00349 (20673) covalent geometry : angle 0.70220 (28035) SS BOND : bond 0.00556 ( 36) SS BOND : angle 1.57405 ( 72) hydrogen bonds : bond 0.04223 ( 720) hydrogen bonds : angle 5.38630 ( 1902) link_ALPHA1-3 : bond 0.01569 ( 3) link_ALPHA1-3 : angle 1.94313 ( 9) link_ALPHA1-6 : bond 0.00858 ( 3) link_ALPHA1-6 : angle 1.33435 ( 9) link_BETA1-4 : bond 0.00563 ( 45) link_BETA1-4 : angle 2.06493 ( 135) link_NAG-ASN : bond 0.00470 ( 54) link_NAG-ASN : angle 3.16921 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8505 (ttt) cc_final: 0.8222 (tpp) REVERT: A 426 MET cc_start: 0.8489 (tpp) cc_final: 0.8069 (tpp) REVERT: A 427 TRP cc_start: 0.7835 (m-10) cc_final: 0.7219 (m-10) REVERT: C 530 MET cc_start: 0.7469 (mmm) cc_final: 0.7057 (mmm) REVERT: C 624 ASP cc_start: 0.7339 (m-30) cc_final: 0.7070 (m-30) REVERT: C 626 MET cc_start: 0.6977 (tmm) cc_final: 0.6613 (tmm) REVERT: C 650 GLN cc_start: 0.6587 (tp40) cc_final: 0.6294 (mm110) REVERT: D 31 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7591 (mtt-85) REVERT: D 52 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8246 (mttt) REVERT: D 75 LEU cc_start: 0.8895 (mm) cc_final: 0.8601 (mt) REVERT: D 80 MET cc_start: 0.8073 (ttm) cc_final: 0.7552 (ttm) REVERT: D 107 THR cc_start: 0.9144 (t) cc_final: 0.8912 (m) REVERT: E 42 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8216 (mp10) REVERT: G 530 MET cc_start: 0.6999 (mmm) cc_final: 0.6776 (mmm) REVERT: G 542 ARG cc_start: 0.5598 (ttt-90) cc_final: 0.5305 (ttp-110) REVERT: G 650 GLN cc_start: 0.6648 (tp40) cc_final: 0.5687 (tp-100) REVERT: G 655 LYS cc_start: 0.7852 (mttp) cc_final: 0.7557 (mttm) REVERT: I 6 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: I 31 ARG cc_start: 0.8434 (ttm110) cc_final: 0.8032 (mtp-110) REVERT: I 75 LEU cc_start: 0.8785 (mm) cc_final: 0.8438 (mt) REVERT: I 102 LEU cc_start: 0.8482 (mt) cc_final: 0.8275 (mt) REVERT: I 107 THR cc_start: 0.9200 (t) cc_final: 0.8780 (p) REVERT: K 42 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7956 (mp10) REVERT: K 71 TYR cc_start: 0.5643 (t80) cc_final: 0.5437 (t80) REVERT: K 86 TYR cc_start: 0.8856 (m-80) cc_final: 0.8373 (m-10) REVERT: F 104 MET cc_start: 0.8590 (ttt) cc_final: 0.8303 (tpp) REVERT: F 426 MET cc_start: 0.8554 (tpp) cc_final: 0.8113 (tpp) REVERT: F 427 TRP cc_start: 0.8024 (m-10) cc_final: 0.7418 (m-10) REVERT: H 542 ARG cc_start: 0.5625 (ttt-90) cc_final: 0.5314 (ttp-110) REVERT: H 590 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7824 (mt0) REVERT: H 626 MET cc_start: 0.7460 (tmm) cc_final: 0.6994 (tmm) REVERT: H 650 GLN cc_start: 0.6723 (tp40) cc_final: 0.5467 (tp-100) REVERT: H 655 LYS cc_start: 0.8199 (tppt) cc_final: 0.7886 (mmtm) REVERT: J 75 LEU cc_start: 0.8757 (mm) cc_final: 0.8461 (mt) REVERT: J 82 LEU cc_start: 0.8754 (mm) cc_final: 0.8446 (mm) REVERT: J 87 THR cc_start: 0.9024 (m) cc_final: 0.8614 (p) REVERT: L 30 TYR cc_start: 0.7565 (m-80) cc_final: 0.7292 (m-80) REVERT: L 42 GLN cc_start: 0.8728 (mp10) cc_final: 0.8306 (mp10) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.1367 time to fit residues: 77.6010 Evaluate side-chains 289 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 161 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 228 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.095062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077654 restraints weight = 57888.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.079820 restraints weight = 35633.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.081374 restraints weight = 25891.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.082257 restraints weight = 20790.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.083007 restraints weight = 18117.071| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20814 Z= 0.157 Angle : 0.748 14.188 28422 Z= 0.359 Chirality : 0.048 0.384 3432 Planarity : 0.004 0.050 3432 Dihedral : 7.653 59.447 4734 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: -0.21 (0.17), residues: 2343 helix: 0.64 (0.25), residues: 423 sheet: 0.28 (0.21), residues: 618 loop : -0.57 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 31 TYR 0.025 0.002 TYR D 100E PHE 0.026 0.001 PHE J 76 TRP 0.037 0.002 TRP B 69 HIS 0.004 0.001 HIS J 79 Details of bonding type rmsd covalent geometry : bond 0.00351 (20673) covalent geometry : angle 0.69285 (28035) SS BOND : bond 0.00544 ( 36) SS BOND : angle 1.53687 ( 72) hydrogen bonds : bond 0.04150 ( 720) hydrogen bonds : angle 5.39805 ( 1902) link_ALPHA1-3 : bond 0.01493 ( 3) link_ALPHA1-3 : angle 1.75894 ( 9) link_ALPHA1-6 : bond 0.00757 ( 3) link_ALPHA1-6 : angle 1.29753 ( 9) link_BETA1-4 : bond 0.00566 ( 45) link_BETA1-4 : angle 2.02441 ( 135) link_NAG-ASN : bond 0.00468 ( 54) link_NAG-ASN : angle 3.22618 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8524 (ttt) cc_final: 0.8237 (tpp) REVERT: A 426 MET cc_start: 0.8492 (tpp) cc_final: 0.7995 (tpp) REVERT: A 427 TRP cc_start: 0.7884 (m-10) cc_final: 0.7197 (m-10) REVERT: A 434 MET cc_start: 0.8420 (ttp) cc_final: 0.8133 (tmm) REVERT: C 530 MET cc_start: 0.7509 (mmm) cc_final: 0.7112 (mmm) REVERT: C 624 ASP cc_start: 0.7271 (m-30) cc_final: 0.7021 (m-30) REVERT: C 626 MET cc_start: 0.7138 (tmm) cc_final: 0.6836 (tmm) REVERT: C 648 GLU cc_start: 0.8796 (pt0) cc_final: 0.8586 (pt0) REVERT: C 649 SER cc_start: 0.8712 (m) cc_final: 0.8063 (t) REVERT: C 650 GLN cc_start: 0.6510 (tp40) cc_final: 0.6285 (mm110) REVERT: D 31 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7202 (mtt-85) REVERT: D 52 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8311 (mttt) REVERT: D 75 LEU cc_start: 0.8856 (mm) cc_final: 0.8619 (mt) REVERT: D 80 MET cc_start: 0.8030 (ttm) cc_final: 0.7573 (ttm) REVERT: D 82 LEU cc_start: 0.8160 (mt) cc_final: 0.7917 (mp) REVERT: D 107 THR cc_start: 0.9107 (t) cc_final: 0.8830 (m) REVERT: E 42 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8182 (mp10) REVERT: E 78 MET cc_start: 0.3149 (mtt) cc_final: 0.2822 (mtt) REVERT: B 112 TRP cc_start: 0.8553 (t-100) cc_final: 0.8244 (t-100) REVERT: G 530 MET cc_start: 0.7127 (mmm) cc_final: 0.6869 (mmm) REVERT: G 542 ARG cc_start: 0.5531 (ttt-90) cc_final: 0.5330 (ttp-110) REVERT: G 650 GLN cc_start: 0.6560 (tp40) cc_final: 0.5544 (tp-100) REVERT: G 655 LYS cc_start: 0.7799 (mttp) cc_final: 0.7516 (mptm) REVERT: I 31 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8059 (mtp-110) REVERT: I 75 LEU cc_start: 0.8687 (mm) cc_final: 0.8296 (mt) REVERT: K 42 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7939 (mp10) REVERT: K 86 TYR cc_start: 0.8824 (m-80) cc_final: 0.8372 (m-10) REVERT: F 104 MET cc_start: 0.8576 (ttt) cc_final: 0.8313 (tpp) REVERT: H 542 ARG cc_start: 0.5653 (ttt-90) cc_final: 0.5303 (ttp-110) REVERT: H 624 ASP cc_start: 0.7000 (m-30) cc_final: 0.6632 (m-30) REVERT: H 626 MET cc_start: 0.7568 (tmm) cc_final: 0.6978 (tmm) REVERT: H 650 GLN cc_start: 0.6789 (tp40) cc_final: 0.5537 (tp-100) REVERT: J 31 ARG cc_start: 0.8328 (tpp80) cc_final: 0.7389 (mtt90) REVERT: J 39 GLN cc_start: 0.8161 (tt0) cc_final: 0.7956 (tt0) REVERT: J 75 LEU cc_start: 0.8791 (mm) cc_final: 0.8488 (mt) REVERT: J 80 MET cc_start: 0.7776 (ttm) cc_final: 0.7472 (ttm) REVERT: J 82 LEU cc_start: 0.8738 (mm) cc_final: 0.8424 (mm) REVERT: J 87 THR cc_start: 0.9031 (m) cc_final: 0.8621 (p) REVERT: L 30 TYR cc_start: 0.7576 (m-80) cc_final: 0.7340 (m-80) REVERT: L 42 GLN cc_start: 0.8715 (mp10) cc_final: 0.8289 (mp10) REVERT: L 86 TYR cc_start: 0.8607 (m-80) cc_final: 0.8389 (m-80) REVERT: L 102 THR cc_start: 0.8592 (p) cc_final: 0.8334 (p) outliers start: 1 outliers final: 1 residues processed: 366 average time/residue: 0.1346 time to fit residues: 79.9674 Evaluate side-chains 299 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 146 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.077050 restraints weight = 58040.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079259 restraints weight = 35246.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080778 restraints weight = 25392.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.081674 restraints weight = 20423.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082384 restraints weight = 17761.910| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20814 Z= 0.174 Angle : 0.765 14.025 28422 Z= 0.368 Chirality : 0.048 0.378 3432 Planarity : 0.005 0.050 3432 Dihedral : 7.691 59.239 4734 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.13 % 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: -0.21 (0.17), residues: 2343 helix: 0.83 (0.26), residues: 405 sheet: 0.25 (0.21), residues: 618 loop : -0.60 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 94 TYR 0.032 0.002 TYR D 100E PHE 0.027 0.002 PHE I 76 TRP 0.035 0.002 TRP G 610 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00394 (20673) covalent geometry : angle 0.71418 (28035) SS BOND : bond 0.00600 ( 36) SS BOND : angle 1.57759 ( 72) hydrogen bonds : bond 0.04199 ( 720) hydrogen bonds : angle 5.39455 ( 1902) link_ALPHA1-3 : bond 0.01654 ( 3) link_ALPHA1-3 : angle 1.77883 ( 9) link_ALPHA1-6 : bond 0.00715 ( 3) link_ALPHA1-6 : angle 1.27865 ( 9) link_BETA1-4 : bond 0.00579 ( 45) link_BETA1-4 : angle 2.03261 ( 135) link_NAG-ASN : bond 0.00492 ( 54) link_NAG-ASN : angle 3.10455 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.00 seconds wall clock time: 54 minutes 51.33 seconds (3291.33 seconds total)