Starting phenix.real_space_refine on Sun Sep 13 03:25:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_7568.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_7568.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_7568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_7568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_7568.map" model { file = "/net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_7568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crq_7568/09_2026/6crq_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 5.18, per 1000 atoms: 0.26 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: 2.40 Conformation dependent library (CDL) restraints added in 827.0 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: 0.83 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: 4.10 Time building geometry restraints manager: 3.07 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 - 17.77: 10983 17.77 - 35.54: 373 35.54 - 53.31: 125 53.31 - 71.08: 46 71.08 - 88.85: 17 Dihedral angle restraints: 11544 sinusoidal: 4692 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 11541 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: 0.02 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.930 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 11.524 88.852 7020 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/Z covalent geometry : bond 0.01507 / 0.79 (20673) covalent geometry : angle 1.49750 / 0.96 (28035) SS BOND : bond 0.15698 / 7.15 ( 36) SS BOND : angle 4.00203 / 2.71 ( 72) hydrogen bonds : bond 0.19954 / 13.33 ( 720) hydrogen bonds : angle 7.54414 / 5.25 ( 1902) link_ALPHA1-3 : bond 0.03597 / 1.80 ( 3) link_ALPHA1-3 : angle 2.06541 / 1.36 ( 9) link_ALPHA1-6 : bond 0.04245 / 2.09 ( 3) link_ALPHA1-6 : angle 3.69472 / 2.56 ( 9) link_BETA1-4 : bond 0.03159 / 2.03 ( 45) link_BETA1-4 : angle 2.72656 / 2.06 ( 135) link_NAG-ASN : bond 0.05191 / 3.44 ( 54) link_NAG-ASN : angle 4.81401 / 3.41 ( 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 : 0.654 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: 0.4026 (p) cc_final: 0.3413 (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: 0.8142 (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: 0.8273 (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: 0.9090 (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: 0.1619 time to fit residues: 178.8840 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 : 0.738 ------------------------------------------------------------------------------- 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: 2.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 99 ASN A 283 ASN A 302 ASN A 425 ASN A 440 GLN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.082433 restraints weight = 56143.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084837 restraints weight = 33790.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086511 restraints weight = 24137.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087659 restraints weight = 19206.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088437 restraints weight = 16372.198| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20814 Z= 0.219 Angle : 0.947 26.960 28422 Z= 0.446 Chirality : 0.053 0.495 3432 Planarity : 0.005 0.055 3432 Dihedral : 5.538 34.249 2559 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.34 % Allowed : 3.17 % Favored : 96.49 % 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: 1.25 (0.17), residues: 2343 helix: 0.76 (0.24), residues: 438 sheet: 0.62 (0.20), residues: 627 loop : 1.19 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 54 TYR 0.026 0.002 TYR A 173 PHE 0.028 0.002 PHE E 49 TRP 0.029 0.003 TRP A 479 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (20673) covalent geometry : angle 0.86856 / 0.43 (28035) SS BOND : bond 0.00593 / 0.34 ( 36) SS BOND : angle 1.55175 / 1.10 ( 72) hydrogen bonds : bond 0.05657 / 3.81 ( 720) hydrogen bonds : angle 5.91545 / 4.06 ( 1902) link_ALPHA1-3 : bond 0.01003 / 0.50 ( 3) link_ALPHA1-3 : angle 1.78889 / 1.33 ( 9) link_ALPHA1-6 : bond 0.02215 / 1.09 ( 3) link_ALPHA1-6 : angle 3.46373 / 2.35 ( 9) link_BETA1-4 : bond 0.00749 / 0.46 ( 45) link_BETA1-4 : angle 2.64436 / 2.02 ( 135) link_NAG-ASN : bond 0.00560 / 0.36 ( 54) link_NAG-ASN : angle 4.35247 / 3.53 ( 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 493 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 486 time to evaluate : 0.811 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: A 84 ILE cc_start: 0.7376 (mp) cc_final: 0.7103 (mm) REVERT: A 182 VAL cc_start: 0.8869 (t) cc_final: 0.8635 (p) REVERT: A 207 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7344 (ptpt) REVERT: C 543 ASN cc_start: 0.8123 (t0) cc_final: 0.7879 (t0) REVERT: C 648 GLU cc_start: 0.8945 (pt0) cc_final: 0.8325 (pt0) REVERT: D 31 ARG cc_start: 0.8391 (tpp80) cc_final: 0.7719 (mtt-85) REVERT: D 73 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.7994 (mtp85) REVERT: D 76 PHE cc_start: 0.8443 (m-80) cc_final: 0.8116 (m-10) REVERT: E 23 CYS cc_start: 0.2358 (p) cc_final: 0.1903 (p) REVERT: E 102 THR cc_start: 0.7889 (p) cc_final: 0.7461 (t) REVERT: B 97 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8286 (ttpt) REVERT: B 103 GLN cc_start: 0.7444 (mt0) cc_final: 0.7077 (tm-30) REVERT: B 107 ASP cc_start: 0.8329 (m-30) cc_final: 0.6890 (m-30) REVERT: G 530 MET cc_start: 0.7259 (mtp) cc_final: 0.6914 (mmm) REVERT: G 607 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7419 (m-40) REVERT: G 621 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6668 (tm-30) REVERT: G 648 GLU cc_start: 0.8859 (pt0) cc_final: 0.8637 (pt0) REVERT: I 31 ARG cc_start: 0.8638 (ttm110) cc_final: 0.7948 (mtm-85) REVERT: I 100 TYR cc_start: 0.7851 (m-80) cc_final: 0.7485 (m-80) REVERT: K 42 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8135 (mp10) REVERT: K 86 TYR cc_start: 0.8715 (m-80) cc_final: 0.8497 (m-80) REVERT: F 99 ASN cc_start: 0.7965 (m-40) cc_final: 0.6981 (m-40) REVERT: F 100 MET cc_start: 0.7685 (mtp) cc_final: 0.7389 (mtp) REVERT: F 103 GLN cc_start: 0.7551 (mp10) cc_final: 0.6386 (mp10) REVERT: F 104 MET cc_start: 0.8090 (ttt) cc_final: 0.7714 (tpp) REVERT: F 161 MET cc_start: 0.7334 (tpt) cc_final: 0.6685 (tpt) REVERT: F 195 ASN cc_start: 0.8622 (t0) cc_final: 0.8266 (t0) REVERT: F 328 GLN cc_start: 0.8526 (tt0) cc_final: 0.8018 (mp10) REVERT: F 341 THR cc_start: 0.9248 (p) cc_final: 0.8917 (t) REVERT: F 494 LEU cc_start: 0.8679 (mt) cc_final: 0.7626 (mt) REVERT: F 502 LYS cc_start: 0.6032 (tppt) cc_final: 0.4860 (tptt) REVERT: H 530 MET cc_start: 0.7248 (mtp) cc_final: 0.6511 (mmm) REVERT: H 620 SER cc_start: 0.8554 (p) cc_final: 0.8304 (p) REVERT: H 645 LEU cc_start: 0.9021 (mt) cc_final: 0.8785 (mt) REVERT: H 648 GLU cc_start: 0.8667 (pt0) cc_final: 0.8158 (pt0) REVERT: J 87 THR cc_start: 0.8840 (m) cc_final: 0.8453 (p) REVERT: J 102 LEU cc_start: 0.8224 (mp) cc_final: 0.7946 (mp) REVERT: L 30 TYR cc_start: 0.7724 (m-80) cc_final: 0.7222 (m-80) REVERT: L 86 TYR cc_start: 0.8848 (m-80) cc_final: 0.8437 (m-10) REVERT: L 96 GLU cc_start: 0.8319 (pt0) cc_final: 0.7942 (pt0) REVERT: L 102 THR cc_start: 0.7935 (p) cc_final: 0.7615 (p) outliers start: 7 outliers final: 3 residues processed: 493 average time/residue: 0.1457 time to fit residues: 111.1934 Evaluate side-chains 328 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 324 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 4.9990 chunk 219 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN ** 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 ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 GLN G 607 ASN F 170 GLN ** F 203 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078012 restraints weight = 56887.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080298 restraints weight = 34486.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.081847 restraints weight = 24952.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.082788 restraints weight = 20129.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083559 restraints weight = 17531.138| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 20814 Z= 0.248 Angle : 0.874 19.918 28422 Z= 0.422 Chirality : 0.052 0.530 3432 Planarity : 0.006 0.086 3432 Dihedral : 5.675 33.162 2559 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % 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: 0.71 (0.17), residues: 2343 helix: 0.87 (0.25), residues: 420 sheet: 0.60 (0.20), residues: 633 loop : 0.40 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG I 94 TYR 0.037 0.002 TYR D 100E PHE 0.019 0.002 PHE B 176 TRP 0.026 0.003 TRP G 610 HIS 0.007 0.002 HIS F 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (20673) covalent geometry : angle 0.81811 / 0.41 (28035) SS BOND : bond 0.00607 / 0.35 ( 36) SS BOND : angle 1.63652 / 1.18 ( 72) hydrogen bonds : bond 0.05450 / 3.67 ( 720) hydrogen bonds : angle 5.71282 / 3.91 ( 1902) link_ALPHA1-3 : bond 0.01476 / 0.74 ( 3) link_ALPHA1-3 : angle 1.07211 / 0.65 ( 9) link_ALPHA1-6 : bond 0.01934 / 0.96 ( 3) link_ALPHA1-6 : angle 2.85370 / 1.90 ( 9) link_BETA1-4 : bond 0.00655 / 0.44 ( 45) link_BETA1-4 : angle 2.31154 / 1.77 ( 135) link_NAG-ASN : bond 0.00809 / 0.52 ( 54) link_NAG-ASN : angle 3.48604 / 2.78 ( 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 423 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 421 time to evaluate : 0.696 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: 0.8208 (ttt) cc_final: 0.7940 (tpp) REVERT: A 182 VAL cc_start: 0.8972 (t) cc_final: 0.8754 (p) REVERT: A 207 LYS cc_start: 0.7775 (mmmt) cc_final: 0.7523 (mtpt) REVERT: C 530 MET cc_start: 0.6998 (mtp) cc_final: 0.6664 (mmm) REVERT: C 645 LEU cc_start: 0.8718 (mt) cc_final: 0.8483 (mt) REVERT: C 648 GLU cc_start: 0.8884 (pt0) cc_final: 0.8314 (pt0) REVERT: D 25 SER cc_start: 0.7674 (m) cc_final: 0.7394 (p) REVERT: E 42 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8189 (mp10) REVERT: B 97 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8403 (mtmt) REVERT: B 107 ASP cc_start: 0.8473 (m-30) cc_final: 0.8035 (t0) REVERT: B 494 LEU cc_start: 0.8467 (mm) cc_final: 0.7608 (mm) REVERT: G 530 MET cc_start: 0.7582 (mtp) cc_final: 0.5858 (mmm) REVERT: G 542 ARG cc_start: 0.5594 (ttt-90) cc_final: 0.5310 (ttp-110) REVERT: G 621 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6630 (tm-30) REVERT: G 648 GLU cc_start: 0.8865 (pt0) cc_final: 0.8495 (pt0) REVERT: G 650 GLN cc_start: 0.6824 (tp40) cc_final: 0.5702 (tp-100) REVERT: I 48 ILE cc_start: 0.9602 (mm) cc_final: 0.9387 (mp) REVERT: I 86 ASP cc_start: 0.8303 (m-30) cc_final: 0.8082 (m-30) REVERT: K 42 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7961 (mp10) REVERT: K 86 TYR cc_start: 0.8802 (m-80) cc_final: 0.8430 (m-10) REVERT: F 104 MET cc_start: 0.8356 (ttt) cc_final: 0.8053 (tpp) REVERT: F 195 ASN cc_start: 0.8461 (t0) cc_final: 0.7913 (t0) REVERT: F 328 GLN cc_start: 0.8737 (tt0) cc_final: 0.8154 (mp10) REVERT: H 530 MET cc_start: 0.7615 (mtp) cc_final: 0.7227 (mmm) REVERT: H 589 ASP cc_start: 0.8581 (t0) cc_final: 0.8324 (t0) REVERT: H 606 THR cc_start: 0.8750 (p) cc_final: 0.8167 (p) REVERT: H 626 MET cc_start: 0.5357 (ttt) cc_final: 0.4155 (ttt) REVERT: H 648 GLU cc_start: 0.8738 (pt0) cc_final: 0.8414 (pt0) REVERT: J 30 GLU cc_start: 0.8123 (tp30) cc_final: 0.7892 (tp30) REVERT: J 57 ASN cc_start: 0.9048 (t0) cc_final: 0.8767 (t0) REVERT: L 30 TYR cc_start: 0.7767 (m-80) cc_final: 0.7405 (m-80) REVERT: L 42 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8205 (mp10) REVERT: L 77 ARG cc_start: 0.7429 (ttp-110) cc_final: 0.7220 (ttp80) REVERT: L 86 TYR cc_start: 0.8935 (m-80) cc_final: 0.8328 (m-10) REVERT: L 102 THR cc_start: 0.7927 (p) cc_final: 0.7564 (p) outliers start: 2 outliers final: 2 residues processed: 422 average time/residue: 0.1413 time to fit residues: 93.6749 Evaluate side-chains 307 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 9.9990 chunk 173 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3457 r_free = 0.3457 target = 0.097274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079137 restraints weight = 56711.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.081490 restraints weight = 34434.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.083053 restraints weight = 24744.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084132 restraints weight = 19904.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084845 restraints weight = 17143.584| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20814 Z= 0.156 Angle : 0.771 17.366 28422 Z= 0.363 Chirality : 0.048 0.367 3432 Planarity : 0.004 0.045 3432 Dihedral : 5.294 31.960 2559 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.14 % Allowed : 1.87 % 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: 0.58 (0.17), residues: 2343 helix: 0.90 (0.25), residues: 441 sheet: 0.60 (0.20), residues: 627 loop : 0.21 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 94 TYR 0.014 0.001 TYR G 638 PHE 0.018 0.002 PHE D 76 TRP 0.032 0.002 TRP G 610 HIS 0.009 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (20673) covalent geometry : angle 0.71584 / 0.35 (28035) SS BOND : bond 0.00675 / 0.44 ( 36) SS BOND : angle 1.63810 / 1.15 ( 72) hydrogen bonds : bond 0.04417 / 3.02 ( 720) hydrogen bonds : angle 5.33675 / 3.68 ( 1902) link_ALPHA1-3 : bond 0.00985 / 0.49 ( 3) link_ALPHA1-3 : angle 1.61473 / 1.13 ( 9) link_ALPHA1-6 : bond 0.02043 / 1.02 ( 3) link_ALPHA1-6 : angle 2.46934 / 1.65 ( 9) link_BETA1-4 : bond 0.00568 / 0.36 ( 45) link_BETA1-4 : angle 2.08836 / 1.61 ( 135) link_NAG-ASN : bond 0.00591 / 0.38 ( 54) link_NAG-ASN : angle 3.22833 / 2.54 ( 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 408 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 405 time to evaluate : 0.780 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: 0.8355 (ttt) cc_final: 0.8103 (tpp) REVERT: A 195 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7983 (t0) REVERT: C 530 MET cc_start: 0.6845 (mtp) cc_final: 0.6097 (mmm) REVERT: C 536 THR cc_start: 0.8591 (m) cc_final: 0.8282 (m) REVERT: C 543 ASN cc_start: 0.8017 (t0) cc_final: 0.7767 (t0) REVERT: C 626 MET cc_start: 0.5053 (ttt) cc_final: 0.4771 (tmm) REVERT: C 648 GLU cc_start: 0.8814 (pt0) cc_final: 0.8601 (pt0) REVERT: D 31 ARG cc_start: 0.8374 (tpp80) cc_final: 0.7722 (mtt-85) REVERT: D 39 GLN cc_start: 0.7734 (tp40) cc_final: 0.7353 (tm-30) REVERT: D 73 ARG cc_start: 0.8468 (ptp-110) cc_final: 0.8252 (mtp85) REVERT: D 80 MET cc_start: 0.8252 (ttm) cc_final: 0.7763 (ttm) REVERT: D 87 THR cc_start: 0.8905 (m) cc_final: 0.8454 (p) REVERT: E 33 MET cc_start: 0.8374 (ttm) cc_final: 0.8105 (mtt) REVERT: E 42 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8158 (mp10) REVERT: B 97 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8441 (mtmt) REVERT: G 542 ARG cc_start: 0.5452 (ttt-90) cc_final: 0.5108 (ttp-110) REVERT: G 589 ASP cc_start: 0.8272 (t0) cc_final: 0.7907 (t0) REVERT: G 621 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6791 (tm-30) REVERT: G 626 MET cc_start: 0.6625 (tmm) cc_final: 0.5814 (ppp) REVERT: G 648 GLU cc_start: 0.8873 (pt0) cc_final: 0.8367 (pt0) REVERT: G 650 GLN cc_start: 0.6790 (tp40) cc_final: 0.5679 (tp-100) REVERT: I 6 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: I 31 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8110 (mtm-85) REVERT: K 66 GLN cc_start: 0.8957 (pm20) cc_final: 0.8570 (pp30) REVERT: K 86 TYR cc_start: 0.8784 (m-80) cc_final: 0.8343 (m-10) REVERT: F 104 MET cc_start: 0.8287 (ttt) cc_final: 0.7897 (tpp) REVERT: F 195 ASN cc_start: 0.8451 (t0) cc_final: 0.7917 (t0) REVERT: F 328 GLN cc_start: 0.8708 (tt0) cc_final: 0.8128 (mp10) REVERT: H 530 MET cc_start: 0.7600 (mtp) cc_final: 0.7289 (mmm) REVERT: H 589 ASP cc_start: 0.8478 (t0) cc_final: 0.8243 (t0) REVERT: H 626 MET cc_start: 0.5075 (ttt) cc_final: 0.4384 (ttt) REVERT: J 57 ASN cc_start: 0.9067 (t0) cc_final: 0.8805 (t0) REVERT: J 86 ASP cc_start: 0.8301 (m-30) cc_final: 0.7913 (m-30) REVERT: J 87 THR cc_start: 0.8913 (m) cc_final: 0.8517 (p) REVERT: L 30 TYR cc_start: 0.7758 (m-80) cc_final: 0.7367 (m-80) REVERT: L 66 GLN cc_start: 0.8985 (pm20) cc_final: 0.8666 (pp30) REVERT: L 86 TYR cc_start: 0.8845 (m-80) cc_final: 0.8413 (m-80) REVERT: L 102 THR cc_start: 0.7948 (p) cc_final: 0.7701 (p) outliers start: 3 outliers final: 0 residues processed: 408 average time/residue: 0.1392 time to fit residues: 89.9248 Evaluate side-chains 299 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 7.9990 chunk 180 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 GLN J 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075341 restraints weight = 57789.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.077475 restraints weight = 35469.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078974 restraints weight = 25899.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079975 restraints weight = 21018.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080571 restraints weight = 18233.761| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20814 Z= 0.265 Angle : 0.874 15.700 28422 Z= 0.416 Chirality : 0.051 0.422 3432 Planarity : 0.005 0.048 3432 Dihedral : 5.779 33.919 2559 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.43 % Rotamer: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.17 % 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: -0.09 (0.17), residues: 2343 helix: 0.45 (0.24), residues: 423 sheet: 0.30 (0.21), residues: 597 loop : -0.32 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 77 TYR 0.038 0.003 TYR D 98 PHE 0.022 0.002 PHE B 176 TRP 0.051 0.002 TRP G 610 HIS 0.007 0.002 HIS I 35A Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (20673) covalent geometry : angle 0.82111 / 0.40 (28035) SS BOND : bond 0.00559 / 0.34 ( 36) SS BOND : angle 1.64048 / 1.13 ( 72) hydrogen bonds : bond 0.05096 / 3.45 ( 720) hydrogen bonds : angle 5.57692 / 3.81 ( 1902) link_ALPHA1-3 : bond 0.01762 / 0.89 ( 3) link_ALPHA1-3 : angle 1.17953 / 0.75 ( 9) link_ALPHA1-6 : bond 0.01561 / 0.78 ( 3) link_ALPHA1-6 : angle 2.10586 / 1.42 ( 9) link_BETA1-4 : bond 0.00636 / 0.44 ( 45) link_BETA1-4 : angle 2.20087 / 1.67 ( 135) link_NAG-ASN : bond 0.01022 / 0.65 ( 54) link_NAG-ASN : angle 3.45440 / 2.67 ( 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 371 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 0.714 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 217 TYR cc_start: 0.8221 (m-80) cc_final: 0.6666 (m-80) REVERT: C 536 THR cc_start: 0.8729 (m) cc_final: 0.8335 (m) REVERT: C 543 ASN cc_start: 0.8187 (t0) cc_final: 0.7984 (t0) REVERT: C 624 ASP cc_start: 0.8000 (m-30) cc_final: 0.7774 (m-30) REVERT: C 648 GLU cc_start: 0.8843 (pt0) cc_final: 0.8287 (pt0) REVERT: D 31 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7769 (mtt-85) REVERT: D 80 MET cc_start: 0.8367 (ttm) cc_final: 0.8008 (ttm) REVERT: E 42 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8181 (mp10) REVERT: E 53 LYS cc_start: 0.8106 (mttp) cc_final: 0.7702 (mttp) REVERT: B 53 PHE cc_start: 0.7857 (m-80) cc_final: 0.7535 (m-10) REVERT: G 530 MET cc_start: 0.7302 (mmm) cc_final: 0.6725 (mmm) REVERT: G 538 THR cc_start: 0.9106 (t) cc_final: 0.8835 (m) REVERT: G 542 ARG cc_start: 0.5644 (ttt-90) cc_final: 0.5261 (ttp-110) REVERT: G 621 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6839 (tm-30) REVERT: G 626 MET cc_start: 0.6137 (tmm) cc_final: 0.5749 (ppp) REVERT: G 648 GLU cc_start: 0.8886 (pt0) cc_final: 0.8380 (pt0) REVERT: G 650 GLN cc_start: 0.6891 (tp40) cc_final: 0.5742 (tp-100) REVERT: I 48 ILE cc_start: 0.9619 (mm) cc_final: 0.9383 (mp) REVERT: I 77 THR cc_start: 0.8754 (p) cc_final: 0.8476 (m) REVERT: I 82 ILE cc_start: 0.8969 (mm) cc_final: 0.8717 (mm) REVERT: K 42 GLN cc_start: 0.8067 (mp10) cc_final: 0.7768 (mp10) REVERT: K 86 TYR cc_start: 0.8919 (m-80) cc_final: 0.8453 (m-10) REVERT: F 104 MET cc_start: 0.8496 (ttt) cc_final: 0.8218 (tpp) REVERT: H 539 VAL cc_start: 0.8324 (t) cc_final: 0.8079 (t) REVERT: H 542 ARG cc_start: 0.5799 (ttt-90) cc_final: 0.5402 (ttp-110) REVERT: J 9 SER cc_start: 0.8581 (p) cc_final: 0.8365 (m) REVERT: J 82 LEU cc_start: 0.8785 (mm) cc_final: 0.8549 (mm) REVERT: J 84 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7825 (tm-30) REVERT: J 86 ASP cc_start: 0.8422 (m-30) cc_final: 0.7901 (m-30) REVERT: L 30 TYR cc_start: 0.7800 (m-80) cc_final: 0.7492 (m-80) REVERT: L 42 GLN cc_start: 0.8694 (mp10) cc_final: 0.8260 (mp10) REVERT: L 102 THR cc_start: 0.8374 (p) cc_final: 0.7966 (p) outliers start: 2 outliers final: 2 residues processed: 371 average time/residue: 0.1278 time to fit residues: 75.9726 Evaluate side-chains 286 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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: 4.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN B 99 ASN B 216 HIS B 425 ASN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.074918 restraints weight = 57427.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.077055 restraints weight = 35392.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078473 restraints weight = 25696.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079484 restraints weight = 20924.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079975 restraints weight = 18127.284| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20814 Z= 0.254 Angle : 0.862 15.063 28422 Z= 0.410 Chirality : 0.051 0.559 3432 Planarity : 0.005 0.047 3432 Dihedral : 5.778 34.460 2559 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.95 % Favored : 95.01 % Rotamer: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % 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: -0.37 (0.17), residues: 2343 helix: 0.35 (0.25), residues: 414 sheet: 0.11 (0.21), residues: 630 loop : -0.57 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 429 TYR 0.022 0.002 TYR D 100E PHE 0.017 0.002 PHE J 76 TRP 0.050 0.002 TRP G 610 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (20673) covalent geometry : angle 0.80975 / 0.40 (28035) SS BOND : bond 0.00670 / 0.41 ( 36) SS BOND : angle 1.54912 / 1.10 ( 72) hydrogen bonds : bond 0.04891 / 3.33 ( 720) hydrogen bonds : angle 5.58185 / 3.82 ( 1902) link_ALPHA1-3 : bond 0.01627 / 0.82 ( 3) link_ALPHA1-3 : angle 1.68250 / 1.17 ( 9) link_ALPHA1-6 : bond 0.01482 / 0.74 ( 3) link_ALPHA1-6 : angle 1.62674 / 1.10 ( 9) link_BETA1-4 : bond 0.00638 / 0.43 ( 45) link_BETA1-4 : angle 2.21889 / 1.68 ( 135) link_NAG-ASN : bond 0.00846 / 0.59 ( 54) link_NAG-ASN : angle 3.36340 / 2.61 ( 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 359 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.768 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: 0.8416 (tpp) cc_final: 0.7879 (tpp) REVERT: A 217 TYR cc_start: 0.8056 (m-80) cc_final: 0.7056 (m-80) REVERT: C 530 MET cc_start: 0.7545 (mmm) cc_final: 0.7338 (mmm) REVERT: C 536 THR cc_start: 0.8697 (m) cc_final: 0.8278 (m) REVERT: C 543 ASN cc_start: 0.8147 (t0) cc_final: 0.7907 (t0) REVERT: C 645 LEU cc_start: 0.8604 (mt) cc_final: 0.8377 (mt) REVERT: C 648 GLU cc_start: 0.8788 (pt0) cc_final: 0.8224 (pt0) REVERT: C 650 GLN cc_start: 0.7095 (tp40) cc_final: 0.6597 (mm110) REVERT: C 655 LYS cc_start: 0.7709 (mttm) cc_final: 0.7213 (mtmm) REVERT: E 42 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8212 (mp10) REVERT: B 53 PHE cc_start: 0.7865 (m-10) cc_final: 0.7578 (m-10) REVERT: G 530 MET cc_start: 0.7247 (mmm) cc_final: 0.6727 (mmm) REVERT: G 538 THR cc_start: 0.9046 (t) cc_final: 0.8787 (m) REVERT: G 542 ARG cc_start: 0.5699 (ttt-90) cc_final: 0.5199 (ttp-110) REVERT: G 626 MET cc_start: 0.6253 (tmm) cc_final: 0.5832 (ppp) REVERT: G 648 GLU cc_start: 0.8892 (pt0) cc_final: 0.8456 (pp20) REVERT: G 650 GLN cc_start: 0.6835 (tp40) cc_final: 0.5620 (tp40) REVERT: I 6 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: I 31 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8079 (mtm-85) REVERT: I 77 THR cc_start: 0.8719 (p) cc_final: 0.8448 (m) REVERT: I 97 PHE cc_start: 0.6549 (m-80) cc_final: 0.6153 (m-80) REVERT: K 42 GLN cc_start: 0.8118 (mp10) cc_final: 0.7554 (mp10) REVERT: K 86 TYR cc_start: 0.8822 (m-80) cc_final: 0.8346 (m-10) REVERT: F 104 MET cc_start: 0.8482 (ttt) cc_final: 0.8144 (tpp) REVERT: H 530 MET cc_start: 0.7659 (mmm) cc_final: 0.7115 (mmm) REVERT: H 542 ARG cc_start: 0.5792 (ttt-90) cc_final: 0.5286 (ttp-110) REVERT: J 82 LEU cc_start: 0.8768 (mm) cc_final: 0.8526 (mm) REVERT: J 86 ASP cc_start: 0.8448 (m-30) cc_final: 0.8009 (m-30) REVERT: J 87 THR cc_start: 0.9017 (m) cc_final: 0.8749 (t) REVERT: L 30 TYR cc_start: 0.7776 (m-80) cc_final: 0.7479 (m-80) REVERT: L 42 GLN cc_start: 0.8741 (mp10) cc_final: 0.8302 (mp10) REVERT: L 66 GLN cc_start: 0.9087 (pm20) cc_final: 0.8573 (pp30) outliers start: 1 outliers final: 0 residues processed: 359 average time/residue: 0.1328 time to fit residues: 76.9256 Evaluate side-chains 275 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 224 optimal weight: 0.0470 chunk 228 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076370 restraints weight = 58006.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078552 restraints weight = 35483.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080079 restraints weight = 25694.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081043 restraints weight = 20661.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081708 restraints weight = 17930.305| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20814 Z= 0.176 Angle : 0.780 14.193 28422 Z= 0.371 Chirality : 0.049 0.510 3432 Planarity : 0.004 0.047 3432 Dihedral : 5.556 33.953 2559 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 0.10 % Allowed : 1.39 % Favored : 98.51 % 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: -0.19 (0.17), residues: 2343 helix: 0.86 (0.26), residues: 402 sheet: 0.23 (0.20), residues: 672 loop : -0.61 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 298 TYR 0.023 0.002 TYR L 71 PHE 0.025 0.002 PHE I 76 TRP 0.051 0.002 TRP G 610 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (20673) covalent geometry : angle 0.73219 / 0.36 (28035) SS BOND : bond 0.00563 / 0.33 ( 36) SS BOND : angle 1.58996 / 1.14 ( 72) hydrogen bonds : bond 0.04373 / 2.98 ( 720) hydrogen bonds : angle 5.37199 / 3.69 ( 1902) link_ALPHA1-3 : bond 0.01416 / 0.71 ( 3) link_ALPHA1-3 : angle 1.66070 / 1.14 ( 9) link_ALPHA1-6 : bond 0.01330 / 0.67 ( 3) link_ALPHA1-6 : angle 1.33566 / 0.88 ( 9) link_BETA1-4 : bond 0.00541 / 0.36 ( 45) link_BETA1-4 : angle 2.06762 / 1.58 ( 135) link_NAG-ASN : bond 0.00565 / 0.37 ( 54) link_NAG-ASN : angle 3.01094 / 2.33 ( 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 366 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 0.727 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: 0.8262 (ttm) cc_final: 0.7904 (ttp) REVERT: A 217 TYR cc_start: 0.8178 (m-80) cc_final: 0.7659 (m-80) REVERT: A 426 MET cc_start: 0.8336 (tpp) cc_final: 0.8047 (tpp) REVERT: A 427 TRP cc_start: 0.7743 (m-10) cc_final: 0.7365 (m-10) REVERT: C 536 THR cc_start: 0.8553 (m) cc_final: 0.8332 (m) REVERT: C 649 SER cc_start: 0.8825 (m) cc_final: 0.8387 (t) REVERT: C 650 GLN cc_start: 0.6832 (tp40) cc_final: 0.6448 (mm110) REVERT: C 655 LYS cc_start: 0.7640 (mttm) cc_final: 0.7184 (mttp) REVERT: D 31 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7701 (mtt-85) REVERT: D 80 MET cc_start: 0.8072 (ttm) cc_final: 0.7621 (ttm) REVERT: D 107 THR cc_start: 0.9061 (t) cc_final: 0.8749 (m) REVERT: E 42 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8222 (mp10) REVERT: G 530 MET cc_start: 0.7395 (mmm) cc_final: 0.6791 (mmm) REVERT: G 542 ARG cc_start: 0.5701 (ttt-90) cc_final: 0.5238 (ttp-110) REVERT: G 626 MET cc_start: 0.6293 (tmm) cc_final: 0.5826 (ppp) REVERT: G 648 GLU cc_start: 0.8796 (pt0) cc_final: 0.8373 (pp20) REVERT: G 650 GLN cc_start: 0.6711 (tp40) cc_final: 0.5564 (tp40) REVERT: I 31 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8207 (mtp-110) REVERT: I 75 LEU cc_start: 0.9014 (mm) cc_final: 0.8752 (mt) REVERT: I 107 THR cc_start: 0.9145 (t) cc_final: 0.8831 (p) REVERT: K 42 GLN cc_start: 0.8175 (mp10) cc_final: 0.7630 (mp10) REVERT: K 86 TYR cc_start: 0.8777 (m-80) cc_final: 0.8415 (m-10) REVERT: F 104 MET cc_start: 0.8581 (ttt) cc_final: 0.8152 (tpp) REVERT: H 542 ARG cc_start: 0.5716 (ttt-90) cc_final: 0.5293 (ttp-110) REVERT: H 590 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7619 (mt0) REVERT: J 80 MET cc_start: 0.7913 (ttm) cc_final: 0.7671 (ttm) REVERT: J 82 LEU cc_start: 0.8744 (mm) cc_final: 0.8542 (mm) REVERT: J 87 THR cc_start: 0.9043 (m) cc_final: 0.8768 (t) REVERT: L 30 TYR cc_start: 0.7734 (m-80) cc_final: 0.7493 (m-80) REVERT: L 42 GLN cc_start: 0.8711 (mp10) cc_final: 0.8231 (mp10) REVERT: L 60 ASP cc_start: 0.7983 (m-30) cc_final: 0.7765 (p0) REVERT: L 102 THR cc_start: 0.8456 (p) cc_final: 0.8255 (p) outliers start: 2 outliers final: 1 residues processed: 366 average time/residue: 0.1346 time to fit residues: 78.9684 Evaluate side-chains 277 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 2.9990 chunk 209 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 162 optimal weight: 0.4980 chunk 186 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076631 restraints weight = 57960.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078667 restraints weight = 36146.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080115 restraints weight = 26611.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081070 restraints weight = 21576.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.081563 restraints weight = 18763.673| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20814 Z= 0.173 Angle : 0.765 13.541 28422 Z= 0.366 Chirality : 0.049 0.494 3432 Planarity : 0.004 0.050 3432 Dihedral : 5.474 33.722 2559 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -0.22 (0.17), residues: 2343 helix: 0.79 (0.25), residues: 420 sheet: 0.27 (0.20), residues: 669 loop : -0.67 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.032 0.002 TYR J 100E PHE 0.019 0.001 PHE I 76 TRP 0.039 0.002 TRP G 610 HIS 0.005 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (20673) covalent geometry : angle 0.72266 / 0.36 (28035) SS BOND : bond 0.00564 / 0.30 ( 36) SS BOND : angle 1.70997 / 1.20 ( 72) hydrogen bonds : bond 0.04275 / 2.91 ( 720) hydrogen bonds : angle 5.28214 / 3.65 ( 1902) link_ALPHA1-3 : bond 0.01346 / 0.67 ( 3) link_ALPHA1-3 : angle 1.45583 / 1.00 ( 9) link_ALPHA1-6 : bond 0.01206 / 0.60 ( 3) link_ALPHA1-6 : angle 1.26385 / 0.88 ( 9) link_BETA1-4 : bond 0.00561 / 0.37 ( 45) link_BETA1-4 : angle 1.98641 / 1.52 ( 135) link_NAG-ASN : bond 0.00554 / 0.35 ( 54) link_NAG-ASN : angle 2.73706 / 2.12 ( 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 360 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.763 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: 0.8364 (ttm) cc_final: 0.7658 (tpp) REVERT: A 217 TYR cc_start: 0.8229 (m-80) cc_final: 0.6831 (m-80) REVERT: A 426 MET cc_start: 0.8420 (tpp) cc_final: 0.8045 (tpp) REVERT: A 427 TRP cc_start: 0.7887 (m-10) cc_final: 0.7367 (m-10) REVERT: A 492 GLU cc_start: 0.8148 (tp30) cc_final: 0.7890 (tp30) REVERT: A 494 LEU cc_start: 0.8165 (pp) cc_final: 0.7534 (pp) REVERT: C 530 MET cc_start: 0.7705 (mmm) cc_final: 0.7042 (mmm) REVERT: C 536 THR cc_start: 0.8563 (m) cc_final: 0.8353 (m) REVERT: C 626 MET cc_start: 0.6871 (tmm) cc_final: 0.6623 (tmm) REVERT: C 649 SER cc_start: 0.8828 (m) cc_final: 0.8326 (t) REVERT: C 650 GLN cc_start: 0.6726 (tp40) cc_final: 0.6423 (mm110) REVERT: D 80 MET cc_start: 0.8077 (ttm) cc_final: 0.7587 (ttm) REVERT: D 107 THR cc_start: 0.9030 (t) cc_final: 0.8696 (m) REVERT: E 42 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8203 (mp10) REVERT: B 482 GLU cc_start: 0.7971 (mp0) cc_final: 0.7744 (mp0) REVERT: G 530 MET cc_start: 0.7455 (mmm) cc_final: 0.6877 (mmm) REVERT: G 542 ARG cc_start: 0.5726 (ttt-90) cc_final: 0.5397 (ttp-110) REVERT: G 626 MET cc_start: 0.6631 (tmm) cc_final: 0.5982 (ppp) REVERT: G 635 ILE cc_start: 0.8758 (pt) cc_final: 0.8104 (pt) REVERT: G 648 GLU cc_start: 0.8767 (pt0) cc_final: 0.8451 (pp20) REVERT: G 650 GLN cc_start: 0.6717 (tp40) cc_final: 0.5587 (tp40) REVERT: G 655 LYS cc_start: 0.7842 (mttp) cc_final: 0.7544 (mptm) REVERT: I 31 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8131 (mtp-110) REVERT: I 75 LEU cc_start: 0.8854 (mm) cc_final: 0.8618 (mt) REVERT: I 107 THR cc_start: 0.9052 (t) cc_final: 0.8832 (m) REVERT: K 42 GLN cc_start: 0.8255 (mp10) cc_final: 0.7744 (mp10) REVERT: K 86 TYR cc_start: 0.8756 (m-80) cc_final: 0.8390 (m-10) REVERT: F 39 TYR cc_start: 0.8171 (m-80) cc_final: 0.7918 (m-80) REVERT: F 104 MET cc_start: 0.8588 (ttt) cc_final: 0.8149 (tpp) REVERT: H 542 ARG cc_start: 0.5768 (ttt-90) cc_final: 0.5388 (ttp-110) REVERT: H 626 MET cc_start: 0.7040 (tmm) cc_final: 0.6409 (tmm) REVERT: J 82 LEU cc_start: 0.8736 (mm) cc_final: 0.8507 (mm) REVERT: J 87 THR cc_start: 0.9041 (m) cc_final: 0.8762 (t) REVERT: L 30 TYR cc_start: 0.7673 (m-80) cc_final: 0.7393 (m-80) REVERT: L 42 GLN cc_start: 0.8717 (mp10) cc_final: 0.8238 (mp10) REVERT: L 60 ASP cc_start: 0.8011 (m-30) cc_final: 0.7802 (p0) REVERT: L 66 GLN cc_start: 0.9004 (pm20) cc_final: 0.8468 (pp30) REVERT: L 86 TYR cc_start: 0.8781 (m-80) cc_final: 0.8525 (m-80) REVERT: L 102 THR cc_start: 0.8513 (p) cc_final: 0.8220 (p) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1327 time to fit residues: 76.9068 Evaluate side-chains 287 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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: 30.0000 chunk 172 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.075356 restraints weight = 57741.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077498 restraints weight = 34893.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078981 restraints weight = 25133.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079975 restraints weight = 20205.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.080619 restraints weight = 17435.020| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20814 Z= 0.215 Angle : 0.801 13.175 28422 Z= 0.385 Chirality : 0.050 0.466 3432 Planarity : 0.005 0.047 3432 Dihedral : 5.591 34.240 2559 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.63 % Favored : 94.28 % Rotamer: Outliers : 0.05 % Allowed : 0.67 % Favored : 99.28 % 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: -0.38 (0.17), residues: 2343 helix: 0.70 (0.25), residues: 402 sheet: 0.16 (0.20), residues: 651 loop : -0.75 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 617 TYR 0.026 0.002 TYR B 173 PHE 0.017 0.002 PHE D 76 TRP 0.033 0.002 TRP G 610 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (20673) covalent geometry : angle 0.76219 / 0.38 (28035) SS BOND : bond 0.00582 / 0.32 ( 36) SS BOND : angle 1.67443 / 1.18 ( 72) hydrogen bonds : bond 0.04550 / 3.08 ( 720) hydrogen bonds : angle 5.52193 / 3.79 ( 1902) link_ALPHA1-3 : bond 0.01626 / 0.82 ( 3) link_ALPHA1-3 : angle 1.43415 / 0.98 ( 9) link_ALPHA1-6 : bond 0.01061 / 0.54 ( 3) link_ALPHA1-6 : angle 1.08678 / 0.74 ( 9) link_BETA1-4 : bond 0.00600 / 0.41 ( 45) link_BETA1-4 : angle 2.01894 / 1.53 ( 135) link_NAG-ASN : bond 0.00617 / 0.39 ( 54) link_NAG-ASN : angle 2.70507 / 2.10 ( 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 358 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.771 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: 0.8400 (ttm) cc_final: 0.7669 (tpp) REVERT: A 217 TYR cc_start: 0.8307 (m-80) cc_final: 0.6890 (m-80) REVERT: A 492 GLU cc_start: 0.8181 (tp30) cc_final: 0.7875 (tp30) REVERT: A 494 LEU cc_start: 0.8256 (pp) cc_final: 0.7547 (pp) REVERT: C 530 MET cc_start: 0.7857 (mmm) cc_final: 0.7411 (mmm) REVERT: C 536 THR cc_start: 0.8621 (m) cc_final: 0.8408 (m) REVERT: C 648 GLU cc_start: 0.8719 (pt0) cc_final: 0.8467 (pt0) REVERT: C 649 SER cc_start: 0.8864 (m) cc_final: 0.8339 (t) REVERT: C 650 GLN cc_start: 0.6751 (tp40) cc_final: 0.6464 (mm110) REVERT: D 6 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: D 75 LEU cc_start: 0.8856 (mm) cc_final: 0.8546 (mt) REVERT: D 80 MET cc_start: 0.8124 (ttm) cc_final: 0.7603 (ttm) REVERT: D 107 THR cc_start: 0.9113 (t) cc_final: 0.8877 (p) REVERT: E 42 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8166 (mp10) REVERT: B 482 GLU cc_start: 0.7986 (mp0) cc_final: 0.7701 (mp0) REVERT: G 530 MET cc_start: 0.7464 (mmm) cc_final: 0.7053 (mmm) REVERT: G 542 ARG cc_start: 0.5744 (ttt-90) cc_final: 0.5508 (ttp-110) REVERT: G 626 MET cc_start: 0.6700 (tmm) cc_final: 0.6143 (ppp) REVERT: G 648 GLU cc_start: 0.8855 (pt0) cc_final: 0.8188 (tm-30) REVERT: G 650 GLN cc_start: 0.6610 (tp40) cc_final: 0.5478 (tp40) REVERT: G 655 LYS cc_start: 0.7839 (mttp) cc_final: 0.7521 (mptm) REVERT: I 31 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8125 (mtp-110) REVERT: I 75 LEU cc_start: 0.8779 (mm) cc_final: 0.8453 (mt) REVERT: I 107 THR cc_start: 0.9138 (t) cc_final: 0.8818 (m) REVERT: K 42 GLN cc_start: 0.8256 (mp10) cc_final: 0.7719 (mp10) REVERT: K 86 TYR cc_start: 0.8818 (m-80) cc_final: 0.8376 (m-10) REVERT: F 39 TYR cc_start: 0.8177 (m-80) cc_final: 0.7973 (m-80) REVERT: F 104 MET cc_start: 0.8638 (ttt) cc_final: 0.8174 (tpp) REVERT: H 542 ARG cc_start: 0.5747 (ttt-90) cc_final: 0.5383 (ttp-110) REVERT: H 606 THR cc_start: 0.7770 (m) cc_final: 0.7383 (p) REVERT: H 626 MET cc_start: 0.7321 (tmm) cc_final: 0.6751 (tmm) REVERT: J 75 LEU cc_start: 0.8872 (mm) cc_final: 0.8595 (mt) REVERT: J 82 LEU cc_start: 0.8738 (mm) cc_final: 0.8432 (mm) REVERT: J 87 THR cc_start: 0.9063 (m) cc_final: 0.8791 (t) REVERT: L 42 GLN cc_start: 0.8689 (mp10) cc_final: 0.8212 (mp10) REVERT: L 60 ASP cc_start: 0.8078 (m-30) cc_final: 0.7805 (p0) REVERT: L 82 ASP cc_start: 0.8231 (m-30) cc_final: 0.8006 (m-30) REVERT: L 102 THR cc_start: 0.8595 (p) cc_final: 0.8290 (p) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1280 time to fit residues: 74.9093 Evaluate side-chains 292 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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: 9.9990 chunk 102 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 193 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076476 restraints weight = 57982.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078665 restraints weight = 35046.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.080161 restraints weight = 25174.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081164 restraints weight = 20238.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.081764 restraints weight = 17463.081| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20814 Z= 0.167 Angle : 0.767 13.749 28422 Z= 0.366 Chirality : 0.049 0.451 3432 Planarity : 0.004 0.045 3432 Dihedral : 5.470 33.318 2559 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % 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: -0.35 (0.17), residues: 2343 helix: 0.85 (0.26), residues: 402 sheet: 0.06 (0.21), residues: 627 loop : -0.68 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 31 TYR 0.033 0.002 TYR D 100E PHE 0.032 0.002 PHE D 97 TRP 0.032 0.002 TRP G 610 HIS 0.005 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (20673) covalent geometry : angle 0.72929 / 0.36 (28035) SS BOND : bond 0.00550 / 0.30 ( 36) SS BOND : angle 1.53533 / 1.09 ( 72) hydrogen bonds : bond 0.04197 / 2.87 ( 720) hydrogen bonds : angle 5.36705 / 3.68 ( 1902) link_ALPHA1-3 : bond 0.01402 / 0.70 ( 3) link_ALPHA1-3 : angle 1.59731 / 1.09 ( 9) link_ALPHA1-6 : bond 0.01016 / 0.51 ( 3) link_ALPHA1-6 : angle 1.09682 / 0.71 ( 9) link_BETA1-4 : bond 0.00549 / 0.37 ( 45) link_BETA1-4 : angle 1.95676 / 1.49 ( 135) link_NAG-ASN : bond 0.00508 / 0.32 ( 54) link_NAG-ASN : angle 2.60876 / 2.03 ( 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 362 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.807 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: 0.8425 (ttm) cc_final: 0.7715 (tpp) REVERT: A 217 TYR cc_start: 0.8255 (m-80) cc_final: 0.6920 (m-80) REVERT: A 434 MET cc_start: 0.8418 (ttp) cc_final: 0.8107 (tmm) REVERT: A 492 GLU cc_start: 0.8188 (tp30) cc_final: 0.7877 (tp30) REVERT: A 494 LEU cc_start: 0.8244 (pp) cc_final: 0.7390 (pp) REVERT: C 530 MET cc_start: 0.7635 (mmm) cc_final: 0.7407 (mmm) REVERT: C 624 ASP cc_start: 0.6998 (m-30) cc_final: 0.6645 (m-30) REVERT: C 626 MET cc_start: 0.7112 (tmm) cc_final: 0.6825 (tmm) REVERT: C 648 GLU cc_start: 0.8856 (pt0) cc_final: 0.8643 (pt0) REVERT: C 649 SER cc_start: 0.8751 (m) cc_final: 0.8103 (t) REVERT: C 650 GLN cc_start: 0.6646 (tp40) cc_final: 0.6301 (mm110) REVERT: D 75 LEU cc_start: 0.8847 (mm) cc_final: 0.8571 (mt) REVERT: D 80 MET cc_start: 0.8109 (ttm) cc_final: 0.7694 (ttm) REVERT: D 107 THR cc_start: 0.9059 (t) cc_final: 0.8754 (m) REVERT: E 42 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8179 (mp10) REVERT: E 53 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7816 (pttm) REVERT: B 318 TYR cc_start: 0.8515 (m-80) cc_final: 0.8220 (m-80) REVERT: B 482 GLU cc_start: 0.7953 (mp0) cc_final: 0.7677 (mp0) REVERT: G 530 MET cc_start: 0.7415 (mmm) cc_final: 0.6927 (mmm) REVERT: G 542 ARG cc_start: 0.5670 (ttt-90) cc_final: 0.5453 (ttp-110) REVERT: G 626 MET cc_start: 0.6715 (tmm) cc_final: 0.6000 (tmm) REVERT: G 648 GLU cc_start: 0.8790 (pt0) cc_final: 0.8302 (pp20) REVERT: G 650 GLN cc_start: 0.6566 (tp40) cc_final: 0.5415 (tp40) REVERT: G 655 LYS cc_start: 0.7893 (mttp) cc_final: 0.7582 (mptm) REVERT: I 31 ARG cc_start: 0.8487 (ttm110) cc_final: 0.8130 (mtp-110) REVERT: I 75 LEU cc_start: 0.8704 (mm) cc_final: 0.8329 (mt) REVERT: I 107 THR cc_start: 0.9117 (t) cc_final: 0.8818 (m) REVERT: K 42 GLN cc_start: 0.8251 (mp10) cc_final: 0.7719 (mp10) REVERT: K 86 TYR cc_start: 0.8769 (m-80) cc_final: 0.8292 (m-10) REVERT: F 104 MET cc_start: 0.8569 (ttt) cc_final: 0.8104 (tpp) REVERT: H 542 ARG cc_start: 0.5767 (ttt-90) cc_final: 0.5377 (ttp-110) REVERT: H 624 ASP cc_start: 0.6928 (m-30) cc_final: 0.6575 (m-30) REVERT: H 626 MET cc_start: 0.7406 (tmm) cc_final: 0.6828 (tmm) REVERT: J 75 LEU cc_start: 0.8889 (mm) cc_final: 0.8603 (mt) REVERT: J 80 MET cc_start: 0.7919 (ttm) cc_final: 0.7633 (ttm) REVERT: J 82 LEU cc_start: 0.8734 (mm) cc_final: 0.8449 (mm) REVERT: J 87 THR cc_start: 0.9046 (m) cc_final: 0.8624 (p) REVERT: L 42 GLN cc_start: 0.8693 (mp10) cc_final: 0.8290 (mp10) REVERT: L 60 ASP cc_start: 0.8001 (m-30) cc_final: 0.7791 (p0) REVERT: L 66 GLN cc_start: 0.8956 (pm20) cc_final: 0.8422 (pp30) REVERT: L 82 ASP cc_start: 0.8277 (m-30) cc_final: 0.8038 (m-30) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.1302 time to fit residues: 76.7232 Evaluate side-chains 291 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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: 8.9990 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 195 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075904 restraints weight = 57427.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078103 restraints weight = 34205.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079608 restraints weight = 24430.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080636 restraints weight = 19597.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081231 restraints weight = 16821.866| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.6546 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= 0.174 Angle : 0.768 12.591 28422 Z= 0.368 Chirality : 0.049 0.437 3432 Planarity : 0.004 0.045 3432 Dihedral : 5.413 32.709 2559 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % 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: -0.35 (0.17), residues: 2343 helix: 0.83 (0.26), residues: 402 sheet: 0.12 (0.21), residues: 621 loop : -0.72 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 61 TYR 0.031 0.002 TYR D 100E PHE 0.021 0.001 PHE J 76 TRP 0.021 0.002 TRP I 23 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (20673) covalent geometry : angle 0.73098 / 0.36 (28035) SS BOND : bond 0.00575 / 0.32 ( 36) SS BOND : angle 1.55023 / 1.09 ( 72) hydrogen bonds : bond 0.04182 / 2.85 ( 720) hydrogen bonds : angle 5.42606 / 3.73 ( 1902) link_ALPHA1-3 : bond 0.01351 / 0.68 ( 3) link_ALPHA1-3 : angle 1.38257 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00949 / 0.48 ( 3) link_ALPHA1-6 : angle 1.10983 / 0.71 ( 9) link_BETA1-4 : bond 0.00558 / 0.37 ( 45) link_BETA1-4 : angle 1.95041 / 1.48 ( 135) link_NAG-ASN : bond 0.00527 / 0.34 ( 54) link_NAG-ASN : angle 2.56763 / 2.00 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.96 seconds wall clock time: 55 minutes 2.13 seconds (3302.13 seconds total)