Starting phenix.real_space_refine on Sat Sep 12 13:43:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.map" model { file = "/net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pw6_20500/09_2026/6pw6_20500.cif" } resolution = 4.5 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= 0.007 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 9903 2.51 5 N 2640 2.21 5 O 3276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s 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: 15942 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 398 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "D" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 398 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 970 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 398 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} 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: 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: 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: "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: 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: "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: 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: "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: 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: "b" 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: "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: 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: "f" 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: "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: 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: "l" 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: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 15942 At special positions: 0 Unit cell: (126.5, 128.8, 123.05, 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 3276 8.00 N 2640 7.00 C 9903 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=1.99 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 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=2.17 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 125 " distance=2.04 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 134 " distance=2.03 Simple disulfide: pdb=" SG CYS G 123 " - pdb=" SG CYS G 139 " distance=2.06 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.08 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=1.99 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.17 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 125 " distance=2.04 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 134 " distance=2.03 Simple disulfide: pdb=" SG CYS H 123 " - pdb=" SG CYS H 139 " distance=2.07 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.08 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=1.99 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.17 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 104 " - pdb=" SG CYS I 125 " distance=2.04 Simple disulfide: pdb=" SG CYS I 114 " - pdb=" SG CYS I 134 " distance=2.03 Simple disulfide: pdb=" SG CYS I 123 " - pdb=" SG CYS I 139 " distance=2.06 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 R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA l 3 " - " MAN l 4 " ALPHA1-6 " BMA L 3 " - " MAN L 4 " " BMA V 3 " - " MAN V 4 " " BMA f 3 " - " MAN f 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 605 " - " ASN A 301 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 332 " " NAG A 612 " - " ASN A 392 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 133 " " NAG A 625 " - " ASN A 137 " " NAG A 630 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG B 704 " - " ASN B 618 " " NAG C 605 " - " ASN C 301 " " NAG C 610 " - " ASN C 295 " " NAG C 611 " - " ASN C 332 " " NAG C 612 " - " ASN C 392 " " NAG C 619 " - " ASN C 355 " " NAG C 620 " - " ASN C 133 " " NAG C 625 " - " ASN C 137 " " NAG C 630 " - " ASN C 339 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 625 " " NAG D 703 " - " ASN D 637 " " NAG D 704 " - " ASN D 618 " " NAG E 605 " - " ASN E 301 " " NAG E 610 " - " ASN E 295 " " NAG E 611 " - " ASN E 332 " " NAG E 612 " - " ASN E 392 " " NAG E 619 " - " ASN E 355 " " NAG E 620 " - " ASN E 133 " " NAG E 625 " - " ASN E 137 " " NAG E 630 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 625 " " NAG F 703 " - " ASN F 637 " " NAG F 704 " - " ASN F 618 " " NAG J 1 " - " ASN A 160 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 88 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN A 448 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 363 " " NAG Y 1 " - " ASN C 88 " " NAG Z 1 " - " ASN C 276 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 197 " " NAG c 1 " - " ASN C 448 " " NAG d 1 " - " ASN E 160 " " NAG e 1 " - " ASN E 156 " " NAG f 1 " - " ASN E 262 " " NAG g 1 " - " ASN E 386 " " NAG h 1 " - " ASN E 363 " " NAG i 1 " - " ASN E 88 " " NAG j 1 " - " ASN E 276 " " NAG k 1 " - " ASN E 234 " " NAG l 1 " - " ASN E 197 " " NAG m 1 " - " ASN E 448 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 588.7 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 28.8% alpha, 49.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.835A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.901A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.376A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 560 Processing helix chain 'B' and resid 562 through 567 removed outlier: 4.101A pdb=" N ILE B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 4.094A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'G' and resid 112 through 119 Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.835A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.900A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.376A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 560 Processing helix chain 'D' and resid 562 through 567 removed outlier: 4.101A pdb=" N ILE D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 4.094A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'H' and resid 112 through 119 Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.836A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 334 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.900A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.376A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 560 Processing helix chain 'F' and resid 562 through 567 removed outlier: 4.101A pdb=" N ILE F 566 " --> pdb=" O LEU F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.094A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 Processing helix chain 'I' and resid 112 through 119 Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.580A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.689A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.680A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 395 removed outlier: 5.043A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.185A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.881A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 374 through 378 removed outlier: 10.617A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 108 through 110 Processing sheet with id=AB4, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.580A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.690A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.680A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 393 through 395 removed outlier: 5.042A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 273 removed outlier: 4.186A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.881A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 374 through 378 removed outlier: 10.617A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AC7, first strand: chain 'E' and resid 494 through 498 Processing sheet with id=AC8, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.580A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.689A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.681A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 393 through 395 removed outlier: 5.042A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.185A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.881A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 374 through 378 removed outlier: 10.617A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.805A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 108 through 110 711 hydrogen bonds defined for protein. 1881 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: 2.90 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2610 1.30 - 1.44: 5136 1.44 - 1.58: 8334 1.58 - 1.73: 17 1.73 - 1.87: 148 Bond restraints: 16245 Sorted by residual: bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.49e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.48e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.48e+01 bond pdb=" CG ARG I 135 " pdb=" CD ARG I 135 " ideal model delta sigma weight residual 1.520 1.356 0.164 3.00e-02 1.11e+03 2.99e+01 bond pdb=" CG ARG H 135 " pdb=" CD ARG H 135 " ideal model delta sigma weight residual 1.520 1.356 0.164 3.00e-02 1.11e+03 2.99e+01 ... (remaining 16240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 17233 1.99 - 3.97: 3731 3.97 - 5.96: 880 5.96 - 7.95: 161 7.95 - 9.93: 33 Bond angle restraints: 22038 Sorted by residual: angle pdb=" N ILE D 635 " pdb=" CA ILE D 635 " pdb=" C ILE D 635 " ideal model delta sigma weight residual 112.17 119.01 -6.84 9.50e-01 1.11e+00 5.18e+01 angle pdb=" N ILE B 635 " pdb=" CA ILE B 635 " pdb=" C ILE B 635 " ideal model delta sigma weight residual 112.17 119.01 -6.84 9.50e-01 1.11e+00 5.18e+01 angle pdb=" N ILE F 635 " pdb=" CA ILE F 635 " pdb=" C ILE F 635 " ideal model delta sigma weight residual 112.17 119.00 -6.83 9.50e-01 1.11e+00 5.17e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.87 127.11 -7.24 1.04e+00 9.25e-01 4.85e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.87 127.11 -7.24 1.04e+00 9.25e-01 4.84e+01 ... (remaining 22033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8523 17.99 - 35.98: 294 35.98 - 53.97: 81 53.97 - 71.96: 24 71.96 - 89.95: 12 Dihedral angle restraints: 8934 sinusoidal: 3624 harmonic: 5310 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.21 43.21 1 1.00e+01 1.00e-02 2.60e+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 -129.18 43.18 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.16 43.16 1 1.00e+01 1.00e-02 2.60e+01 ... (remaining 8931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2133 0.128 - 0.256: 546 0.256 - 0.384: 61 0.384 - 0.512: 11 0.512 - 0.640: 3 Chirality restraints: 2754 Sorted by residual: chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.87e+02 chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 ... (remaining 2751 not shown) Planarity restraints: 2751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.130 2.00e-02 2.50e+03 1.07e-01 1.44e+02 pdb=" C7 NAG J 1 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.171 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " 0.130 2.00e-02 2.50e+03 1.07e-01 1.44e+02 pdb=" C7 NAG d 1 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " -0.171 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.130 2.00e-02 2.50e+03 1.07e-01 1.43e+02 pdb=" C7 NAG T 1 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.097 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.021 2.00e-02 2.50e+03 ... (remaining 2748 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2838 2.74 - 3.28: 15132 3.28 - 3.82: 26887 3.82 - 4.36: 32458 4.36 - 4.90: 51372 Nonbonded interactions: 128687 Sorted by model distance: nonbonded pdb=" OG1 THR A 373 " pdb=" O CYS A 385 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR E 373 " pdb=" O CYS E 385 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR C 373 " pdb=" O CYS C 385 " model vdw 2.201 3.040 nonbonded pdb=" O5 NAG N 1 " pdb=" O6 NAG N 1 " model vdw 2.341 2.432 nonbonded pdb=" O5 NAG X 1 " pdb=" O6 NAG X 1 " model vdw 2.341 2.432 ... (remaining 128682 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' } ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'V' selection = chain 'b' selection = chain 'f' selection = chain 'l' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'm' } pdb_interpretation.ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'V' selection = chain 'b' selection = chain 'f' selection = chain 'l' } Set refine NCS operators NCS operators will be refined. 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: 1.340 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.022 0.164 16392 Z= 1.187 Angle : 1.864 9.931 22440 Z= 1.141 Chirality : 0.111 0.640 2754 Planarity : 0.011 0.107 2685 Dihedral : 10.812 89.954 5385 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.17 % Rotamer: Outliers : 0.56 % Allowed : 1.31 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1800 helix: 0.22 (0.24), residues: 384 sheet: 0.80 (0.23), residues: 456 loop : 0.29 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 135 TYR 0.033 0.008 TYR E 173 PHE 0.028 0.007 PHE E 210 TRP 0.030 0.009 TRP E 427 HIS 0.011 0.003 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02170 / 1.18 (16245) covalent geometry : angle 1.83085 / 1.14 (22038) SS BOND : bond 0.04305 / 2.84 ( 39) SS BOND : angle 2.86410 / 1.95 ( 78) hydrogen bonds : bond 0.16174 / 10.50 ( 588) hydrogen bonds : angle 6.96389 / 4.78 ( 1881) link_ALPHA1-3 : bond 0.03039 / 1.52 ( 3) link_ALPHA1-3 : angle 4.78810 / 3.22 ( 9) link_ALPHA1-6 : bond 0.03128 / 1.57 ( 3) link_ALPHA1-6 : angle 2.80576 / 1.87 ( 9) link_BETA1-4 : bond 0.02870 / 1.70 ( 36) link_BETA1-4 : angle 4.50253 / 3.17 ( 108) link_NAG-ASN : bond 0.03016 / 1.84 ( 66) link_NAG-ASN : angle 2.23416 / 1.55 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.145 Fit side-chains REVERT: A 50 THR cc_start: 0.9284 (t) cc_final: 0.8997 (t) REVERT: A 93 PHE cc_start: 0.8221 (m-80) cc_final: 0.7375 (m-80) REVERT: A 95 MET cc_start: 0.8869 (ptt) cc_final: 0.8353 (ptt) REVERT: A 100 MET cc_start: 0.8999 (mtp) cc_final: 0.8533 (mtp) REVERT: A 112 TRP cc_start: 0.8584 (t-100) cc_final: 0.8346 (t-100) REVERT: A 170 GLN cc_start: 0.8361 (pt0) cc_final: 0.8005 (pt0) REVERT: A 184 ILE cc_start: 0.8526 (mt) cc_final: 0.8200 (mt) REVERT: A 197 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 275 GLU cc_start: 0.8984 (tt0) cc_final: 0.8681 (pp20) REVERT: A 307 ILE cc_start: 0.9433 (mt) cc_final: 0.9216 (tp) REVERT: A 426 MET cc_start: 0.8405 (ttm) cc_final: 0.7967 (ttm) outliers start: 3 outliers final: 1 residues processed: 114 average time/residue: 0.0642 time to fit residues: 9.2010 Evaluate side-chains 53 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.139 Evaluate side-chains 53 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7937 (mtm) cc_final: 0.7257 (mtm) REVERT: B 570 VAL cc_start: 0.7878 (m) cc_final: 0.7532 (p) REVERT: B 639 THR cc_start: 0.9320 (m) cc_final: 0.8675 (p) REVERT: B 659 ASP cc_start: 0.8261 (m-30) cc_final: 0.7959 (t70) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0687 time to fit residues: 3.9548 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.026 Evaluate side-chains 27 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.017 Fit side-chains revert: symmetry clash REVERT: G 108 TYR cc_start: 0.9113 (m-80) cc_final: 0.8769 (m-10) REVERT: G 111 ASN cc_start: 0.9298 (t0) cc_final: 0.8928 (t0) REVERT: G 113 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8538 (tmm-80) REVERT: G 128 ASP cc_start: 0.8310 (m-30) cc_final: 0.8006 (m-30) REVERT: G 129 ARG cc_start: 0.8292 (ptt-90) cc_final: 0.7504 (ttt180) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1035 time to fit residues: 2.8759 Evaluate side-chains 19 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0040 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.0570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS A 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.069960 restraints weight = 11654.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072274 restraints weight = 6339.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073982 restraints weight = 4024.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075266 restraints weight = 2796.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076144 restraints weight = 2072.060| |-----------------------------------------------------------------------------| r_work (final): 0.3112 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061564 restraints weight = 4968.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062993 restraints weight = 3077.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063974 restraints weight = 2155.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064670 restraints weight = 1664.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065156 restraints weight = 1384.178| |-----------------------------------------------------------------------------| r_work (final): 0.3080 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.072026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.064789 restraints weight = 1488.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.066418 restraints weight = 740.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.067435 restraints weight = 436.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.067989 restraints weight = 299.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068560 restraints weight = 237.452| |-----------------------------------------------------------------------------| r_work (final): 0.3050 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.066459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.058237 restraints weight = 91.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058947 restraints weight = 42.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.059652 restraints weight = 24.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.060060 restraints weight = 15.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.060361 restraints weight = 11.141| |-----------------------------------------------------------------------------| r_work (final): 0.2690 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103614 restraints weight = 173.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104757 restraints weight = 90.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105550 restraints weight = 61.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106022 restraints weight = 45.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106022 restraints weight = 36.747| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.517 16392 Z= 0.597 Angle : 1.616 43.754 22440 Z= 0.704 Chirality : 0.068 0.370 2754 Planarity : 0.010 0.186 2685 Dihedral : 6.111 34.421 1962 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.33 % Favored : 96.33 % Rotamer: Outliers : 0.94 % Allowed : 3.75 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1800 helix: 1.17 (0.26), residues: 387 sheet: 0.41 (0.24), residues: 435 loop : -0.36 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG C 166 TYR 0.035 0.004 TYR G 133 PHE 0.023 0.003 PHE A 210 TRP 0.059 0.004 TRP F 610 HIS 0.006 0.002 HIS G 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.34 (16245) covalent geometry : angle 1.27818 / 0.62 (22038) SS BOND : bond 0.00644 / 0.39 ( 39) SS BOND : angle 2.70362 / 1.67 ( 78) hydrogen bonds : bond 0.10047 / 6.81 ( 588) hydrogen bonds : angle 5.61032 / 3.88 ( 1881) link_ALPHA1-3 : bond 0.51696 / 25.91 ( 3) link_ALPHA1-3 : angle 15.05236 / 10.14 ( 9) link_ALPHA1-6 : bond 0.50102 / 25.11 ( 3) link_ALPHA1-6 : angle 34.56610 / 21.44 ( 9) link_BETA1-4 : bond 0.01336 / 0.76 ( 36) link_BETA1-4 : angle 4.55028 / 3.61 ( 108) link_NAG-ASN : bond 0.01377 / 0.83 ( 66) link_NAG-ASN : angle 5.93669 / 3.93 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: E 155 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8279 (mmtp) REVERT: E 170 GLN cc_start: 0.8315 (pt0) cc_final: 0.7989 (pt0) REVERT: E 258 GLN cc_start: 0.9223 (mt0) cc_final: 0.8934 (mt0) REVERT: E 259 LEU cc_start: 0.9533 (mt) cc_final: 0.9322 (mm) REVERT: E 275 GLU cc_start: 0.9025 (tt0) cc_final: 0.8822 (pp20) REVERT: E 373 THR cc_start: 0.9014 (t) cc_final: 0.8740 (t) REVERT: E 395 TRP cc_start: 0.8533 (m100) cc_final: 0.8166 (m100) REVERT: E 426 MET cc_start: 0.8243 (ttm) cc_final: 0.7674 (ttm) outliers start: 4 outliers final: 0 residues processed: 85 average time/residue: 0.0504 time to fit residues: 5.5412 Evaluate side-chains 48 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.112 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.038 Fit side-chains REVERT: D 522 PHE cc_start: 0.7339 (t80) cc_final: 0.6890 (t80) REVERT: D 570 VAL cc_start: 0.7764 (m) cc_final: 0.7537 (p) REVERT: D 602 LEU cc_start: 0.8453 (mm) cc_final: 0.8081 (tp) REVERT: D 634 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8372 (tp30) REVERT: D 654 GLU cc_start: 0.9353 (tp30) cc_final: 0.8996 (tp30) REVERT: D 655 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8617 (mtpp) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0527 time to fit residues: 1.9973 Evaluate side-chains 24 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.043 Evaluate side-chains 22 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 111 ASN cc_start: 0.9201 (t0) cc_final: 0.8660 (t0) REVERT: H 113 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8392 (tmm-80) REVERT: H 114 CYS cc_start: 0.6407 (m) cc_final: 0.5702 (m) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0773 time to fit residues: 1.7738 Evaluate side-chains 12 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 173 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 155 optimal weight: 0.0020 chunk 25 optimal weight: 6.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.067607 restraints weight = 11804.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.069775 restraints weight = 6627.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.071252 restraints weight = 4296.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.072396 restraints weight = 3089.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073215 restraints weight = 2350.112| |-----------------------------------------------------------------------------| r_work (final): 0.3052 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060531 restraints weight = 5205.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.061892 restraints weight = 3132.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.062962 restraints weight = 2201.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.063648 restraints weight = 1685.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.064172 restraints weight = 1402.406| |-----------------------------------------------------------------------------| r_work (final): 0.3039 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062984 restraints weight = 1819.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064397 restraints weight = 817.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065282 restraints weight = 448.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065584 restraints weight = 283.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066173 restraints weight = 229.260| |-----------------------------------------------------------------------------| r_work (final): 0.3069 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.062431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.053970 restraints weight = 135.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.054975 restraints weight = 32.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.055398 restraints weight = 14.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.055614 restraints weight = 9.318 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.055656 restraints weight = 7.365 | |-----------------------------------------------------------------------------| r_work (final): 0.2591 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.106467 restraints weight = 232.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107152 restraints weight = 148.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.107858 restraints weight = 116.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108430 restraints weight = 98.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108725 restraints weight = 86.533| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.495 16392 Z= 0.567 Angle : 1.405 43.647 22440 Z= 0.604 Chirality : 0.059 0.425 2754 Planarity : 0.006 0.053 2685 Dihedral : 6.323 37.074 1962 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 0.38 % Allowed : 4.69 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.32 (0.18), residues: 1800 helix: 0.26 (0.24), residues: 393 sheet: 0.27 (0.24), residues: 411 loop : -0.55 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 166 TYR 0.022 0.003 TYR H 142 PHE 0.012 0.003 PHE I 130 TRP 0.024 0.003 TRP B 623 HIS 0.014 0.003 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.31 (16245) covalent geometry : angle 1.07559 / 0.52 (22038) SS BOND : bond 0.00589 / 0.40 ( 39) SS BOND : angle 1.69574 / 1.10 ( 78) hydrogen bonds : bond 0.07128 / 4.69 ( 588) hydrogen bonds : angle 5.42595 / 3.76 ( 1881) link_ALPHA1-3 : bond 0.49197 / 24.66 ( 3) link_ALPHA1-3 : angle 15.73902 / 10.53 ( 9) link_ALPHA1-6 : bond 0.49542 / 24.83 ( 3) link_ALPHA1-6 : angle 33.76112 / 20.84 ( 9) link_BETA1-4 : bond 0.00521 / 0.29 ( 36) link_BETA1-4 : angle 2.89283 / 2.17 ( 108) link_NAG-ASN : bond 0.00801 / 0.45 ( 66) link_NAG-ASN : angle 5.12556 / 3.36 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.133 Fit side-chains REVERT: E 95 MET cc_start: 0.8577 (ptt) cc_final: 0.7924 (ptt) REVERT: E 112 TRP cc_start: 0.8826 (t-100) cc_final: 0.8048 (t-100) REVERT: E 170 GLN cc_start: 0.8179 (pt0) cc_final: 0.7947 (pt0) REVERT: E 275 GLU cc_start: 0.9120 (tt0) cc_final: 0.8758 (pp20) REVERT: E 370 GLU cc_start: 0.8724 (pm20) cc_final: 0.8378 (pt0) REVERT: E 426 MET cc_start: 0.8581 (ttm) cc_final: 0.7553 (ttm) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.0579 time to fit residues: 4.8285 Evaluate side-chains 36 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.139 Evaluate side-chains 31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.037 Fit side-chains REVERT: D 522 PHE cc_start: 0.7605 (t80) cc_final: 0.7210 (t80) REVERT: D 570 VAL cc_start: 0.7744 (m) cc_final: 0.7470 (p) REVERT: D 588 ARG cc_start: 0.9149 (mtp85) cc_final: 0.8785 (mmm-85) REVERT: D 626 MET cc_start: 0.7720 (mtm) cc_final: 0.7453 (mtm) REVERT: D 633 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9301 (tppt) REVERT: D 634 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8484 (tp30) REVERT: D 654 GLU cc_start: 0.9353 (tp30) cc_final: 0.9027 (tp30) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0662 time to fit residues: 2.2383 Evaluate side-chains 22 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.040 Evaluate side-chains 22 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 108 TYR cc_start: 0.8997 (m-80) cc_final: 0.8761 (m-10) REVERT: G 111 ASN cc_start: 0.8958 (t0) cc_final: 0.8550 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0739 time to fit residues: 1.6933 Evaluate side-chains 15 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 7 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.077160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.066198 restraints weight = 12307.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.068223 restraints weight = 6956.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.069712 restraints weight = 4587.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070849 restraints weight = 3327.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.071562 restraints weight = 2563.850| |-----------------------------------------------------------------------------| r_work (final): 0.3002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.059509 restraints weight = 4864.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.060941 restraints weight = 3066.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062004 restraints weight = 2151.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.062727 restraints weight = 1642.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.063282 restraints weight = 1347.940| |-----------------------------------------------------------------------------| r_work (final): 0.3053 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.060368 restraints weight = 1876.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061941 restraints weight = 928.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062979 restraints weight = 553.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063604 restraints weight = 368.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064010 restraints weight = 267.512| |-----------------------------------------------------------------------------| r_work (final): 0.3031 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.044702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2310 r_free = 0.2310 target = 0.043126 restraints weight = 152.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.043669 restraints weight = 31.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.043846 restraints weight = 11.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.044004 restraints weight = 6.523 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.044004 restraints weight = 3.896 | |-----------------------------------------------------------------------------| r_work (final): 0.2421 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110785 restraints weight = 231.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111306 restraints weight = 93.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111612 restraints weight = 56.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111870 restraints weight = 37.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112005 restraints weight = 26.288| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.496 16392 Z= 0.583 Angle : 1.378 43.303 22440 Z= 0.584 Chirality : 0.059 0.423 2754 Planarity : 0.009 0.145 2685 Dihedral : 6.396 37.267 1962 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 0.38 % Allowed : 3.75 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.43 (0.18), residues: 1800 helix: 0.46 (0.26), residues: 375 sheet: 0.10 (0.24), residues: 399 loop : -0.69 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG C 166 TYR 0.015 0.002 TYR E 39 PHE 0.012 0.002 PHE E 288 TRP 0.019 0.003 TRP D 614 HIS 0.016 0.003 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.34 (16245) covalent geometry : angle 1.05249 / 0.50 (22038) SS BOND : bond 0.01340 / 0.84 ( 39) SS BOND : angle 1.50781 / 0.97 ( 78) hydrogen bonds : bond 0.06844 / 4.48 ( 588) hydrogen bonds : angle 5.25763 / 3.66 ( 1881) link_ALPHA1-3 : bond 0.48694 / 24.41 ( 3) link_ALPHA1-3 : angle 15.94888 / 10.69 ( 9) link_ALPHA1-6 : bond 0.49631 / 24.88 ( 3) link_ALPHA1-6 : angle 33.76838 / 20.86 ( 9) link_BETA1-4 : bond 0.00643 / 0.39 ( 36) link_BETA1-4 : angle 2.67582 / 1.98 ( 108) link_NAG-ASN : bond 0.00647 / 0.35 ( 66) link_NAG-ASN : angle 4.87999 / 3.20 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: C 108 ILE cc_start: 0.9314 (mm) cc_final: 0.9052 (mt) REVERT: C 112 TRP cc_start: 0.8837 (t-100) cc_final: 0.8419 (t-100) REVERT: C 195 ASN cc_start: 0.8150 (m-40) cc_final: 0.7913 (m-40) REVERT: C 275 GLU cc_start: 0.9092 (tt0) cc_final: 0.8629 (pp20) REVERT: C 370 GLU cc_start: 0.8746 (pm20) cc_final: 0.8450 (pt0) REVERT: C 426 MET cc_start: 0.8549 (ttm) cc_final: 0.8086 (ttm) REVERT: C 434 MET cc_start: 0.8260 (ttm) cc_final: 0.7119 (mtm) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.0395 time to fit residues: 3.2766 Evaluate side-chains 41 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.137 Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.039 Fit side-chains REVERT: F 522 PHE cc_start: 0.7866 (t80) cc_final: 0.7523 (t80) REVERT: F 570 VAL cc_start: 0.7832 (m) cc_final: 0.7627 (p) REVERT: F 626 MET cc_start: 0.7691 (mtm) cc_final: 0.7127 (mtm) REVERT: F 633 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9290 (tppt) REVERT: F 634 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8603 (tp30) REVERT: F 654 GLU cc_start: 0.9289 (tp30) cc_final: 0.8833 (tp30) REVERT: F 655 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8612 (mtpp) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0548 time to fit residues: 1.8214 Evaluate side-chains 21 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.036 Evaluate side-chains 20 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0515 time to fit residues: 1.0898 Evaluate side-chains 16 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 77 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.077733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.066845 restraints weight = 11765.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.069032 restraints weight = 6355.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070480 restraints weight = 4067.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071627 restraints weight = 2913.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072507 restraints weight = 2210.926| |-----------------------------------------------------------------------------| r_work (final): 0.3022 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.071208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059710 restraints weight = 5204.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061190 restraints weight = 3124.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062228 restraints weight = 2179.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.062910 restraints weight = 1668.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063113 restraints weight = 1387.256| |-----------------------------------------------------------------------------| r_work (final): 0.3034 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061735 restraints weight = 1901.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063408 restraints weight = 828.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064377 restraints weight = 446.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.064872 restraints weight = 278.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065470 restraints weight = 208.173| |-----------------------------------------------------------------------------| r_work (final): 0.3072 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.044928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.043811 restraints weight = 136.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2326 r_free = 0.2326 target = 0.044147 restraints weight = 28.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.044367 restraints weight = 11.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.044367 restraints weight = 5.565 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.044367 restraints weight = 5.564 | |-----------------------------------------------------------------------------| r_work (final): 0.2451 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113186 restraints weight = 224.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113692 restraints weight = 106.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114035 restraints weight = 66.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114298 restraints weight = 48.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114497 restraints weight = 36.465| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.496 16392 Z= 0.533 Angle : 1.315 43.180 22440 Z= 0.551 Chirality : 0.056 0.393 2754 Planarity : 0.006 0.078 2685 Dihedral : 6.266 37.121 1962 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 2.81 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1800 helix: 0.52 (0.26), residues: 375 sheet: -0.05 (0.23), residues: 432 loop : -0.65 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 166 TYR 0.039 0.003 TYR A 217 PHE 0.014 0.002 PHE C 376 TRP 0.015 0.002 TRP B 623 HIS 0.012 0.002 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (16245) covalent geometry : angle 0.98252 / 0.47 (22038) SS BOND : bond 0.00649 / 0.34 ( 39) SS BOND : angle 1.37736 / 0.90 ( 78) hydrogen bonds : bond 0.06386 / 4.22 ( 588) hydrogen bonds : angle 5.14668 / 3.58 ( 1881) link_ALPHA1-3 : bond 0.48380 / 24.25 ( 3) link_ALPHA1-3 : angle 15.88709 / 10.65 ( 9) link_ALPHA1-6 : bond 0.49600 / 24.86 ( 3) link_ALPHA1-6 : angle 33.56478 / 20.72 ( 9) link_BETA1-4 : bond 0.00485 / 0.29 ( 36) link_BETA1-4 : angle 2.35846 / 1.75 ( 108) link_NAG-ASN : bond 0.00693 / 0.39 ( 66) link_NAG-ASN : angle 4.68483 / 3.07 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: C 112 TRP cc_start: 0.8829 (t-100) cc_final: 0.8450 (t-100) REVERT: C 195 ASN cc_start: 0.8088 (m-40) cc_final: 0.7854 (m-40) REVERT: C 318 TYR cc_start: 0.8819 (m-80) cc_final: 0.8235 (m-80) REVERT: C 370 GLU cc_start: 0.8650 (pm20) cc_final: 0.8372 (pt0) REVERT: C 426 MET cc_start: 0.8573 (ttm) cc_final: 0.8281 (ttm) REVERT: C 434 MET cc_start: 0.8790 (ttm) cc_final: 0.7700 (mtp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.0369 time to fit residues: 3.8297 Evaluate side-chains 48 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.122 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.047 Fit side-chains REVERT: F 522 PHE cc_start: 0.7984 (t80) cc_final: 0.7591 (t80) REVERT: F 602 LEU cc_start: 0.8230 (mm) cc_final: 0.7986 (tp) REVERT: F 626 MET cc_start: 0.7602 (mtm) cc_final: 0.6946 (mtm) REVERT: F 633 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9234 (tppt) REVERT: F 634 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8588 (tp30) REVERT: F 654 GLU cc_start: 0.9270 (tp30) cc_final: 0.8782 (tp30) REVERT: F 655 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8595 (mtpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0719 time to fit residues: 2.1975 Evaluate side-chains 21 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.041 Evaluate side-chains 17 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0467 time to fit residues: 0.8502 Evaluate side-chains 13 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0008 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 115 optimal weight: 7.9990 chunk 143 optimal weight: 0.0170 chunk 152 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 0.0670 chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.067610 restraints weight = 11908.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069793 restraints weight = 6540.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.071344 restraints weight = 4229.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072422 restraints weight = 3000.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073215 restraints weight = 2290.043| |-----------------------------------------------------------------------------| r_work (final): 0.3044 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061476 restraints weight = 5116.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063034 restraints weight = 3072.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064103 restraints weight = 2116.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064793 restraints weight = 1618.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065322 restraints weight = 1347.635| |-----------------------------------------------------------------------------| r_work (final): 0.3073 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.068540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062878 restraints weight = 1713.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064573 restraints weight = 794.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.065582 restraints weight = 434.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.065994 restraints weight = 270.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.066594 restraints weight = 204.735| |-----------------------------------------------------------------------------| r_work (final): 0.3072 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.047439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.045296 restraints weight = 133.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.045804 restraints weight = 29.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.046093 restraints weight = 13.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.046093 restraints weight = 7.203 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.046093 restraints weight = 7.203 | |-----------------------------------------------------------------------------| r_work (final): 0.2489 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115040 restraints weight = 262.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115967 restraints weight = 134.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116389 restraints weight = 88.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.116691 restraints weight = 67.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116967 restraints weight = 53.944| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.499 16392 Z= 0.510 Angle : 1.276 43.104 22440 Z= 0.531 Chirality : 0.058 0.401 2754 Planarity : 0.005 0.062 2685 Dihedral : 6.150 36.896 1962 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.43 (0.19), residues: 1800 helix: 0.39 (0.26), residues: 393 sheet: -0.08 (0.24), residues: 411 loop : -0.59 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 129 TYR 0.024 0.003 TYR E 217 PHE 0.016 0.002 PHE C 376 TRP 0.016 0.002 TRP E 69 HIS 0.011 0.002 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (16245) covalent geometry : angle 0.93444 / 0.45 (22038) SS BOND : bond 0.00280 / 0.17 ( 39) SS BOND : angle 1.34715 / 0.87 ( 78) hydrogen bonds : bond 0.06195 / 4.08 ( 588) hydrogen bonds : angle 5.10340 / 3.55 ( 1881) link_ALPHA1-3 : bond 0.48614 / 24.37 ( 3) link_ALPHA1-3 : angle 16.02370 / 10.74 ( 9) link_ALPHA1-6 : bond 0.49885 / 25.00 ( 3) link_ALPHA1-6 : angle 33.53220 / 20.69 ( 9) link_BETA1-4 : bond 0.00493 / 0.30 ( 36) link_BETA1-4 : angle 2.21644 / 1.66 ( 108) link_NAG-ASN : bond 0.00983 / 0.66 ( 66) link_NAG-ASN : angle 4.58998 / 3.02 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: C 104 MET cc_start: 0.9014 (tpp) cc_final: 0.8805 (tpp) REVERT: C 195 ASN cc_start: 0.8229 (m-40) cc_final: 0.8019 (m-40) REVERT: C 370 GLU cc_start: 0.8652 (pm20) cc_final: 0.8441 (pt0) REVERT: C 426 MET cc_start: 0.8645 (ttm) cc_final: 0.8341 (ttm) REVERT: C 434 MET cc_start: 0.8498 (ttm) cc_final: 0.7278 (mtm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0430 time to fit residues: 3.9858 Evaluate side-chains 42 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.159 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.038 Fit side-chains REVERT: F 522 PHE cc_start: 0.7870 (t80) cc_final: 0.7435 (t80) REVERT: F 588 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8553 (mmm-85) REVERT: F 589 ASP cc_start: 0.9025 (m-30) cc_final: 0.8620 (m-30) REVERT: F 626 MET cc_start: 0.7717 (mtm) cc_final: 0.7111 (mtm) REVERT: F 633 LYS cc_start: 0.9500 (mmmm) cc_final: 0.9227 (tppt) REVERT: F 634 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8540 (tp30) REVERT: F 654 GLU cc_start: 0.9274 (tp30) cc_final: 0.8800 (tp30) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0617 time to fit residues: 1.9052 Evaluate side-chains 21 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.038 Evaluate side-chains 18 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0480 time to fit residues: 0.9205 Evaluate side-chains 17 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 14 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 108 optimal weight: 0.0770 chunk 115 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 11 optimal weight: 0.0010 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.0270 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.079412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068485 restraints weight = 11401.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.070620 restraints weight = 6310.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072152 restraints weight = 4078.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073317 restraints weight = 2880.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074224 restraints weight = 2181.076| |-----------------------------------------------------------------------------| r_work (final): 0.3062 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.071895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.060954 restraints weight = 5018.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062521 restraints weight = 2901.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063545 restraints weight = 1970.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.064283 restraints weight = 1507.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.064769 restraints weight = 1240.766| |-----------------------------------------------------------------------------| r_work (final): 0.3071 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064641 restraints weight = 1996.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065968 restraints weight = 977.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.066811 restraints weight = 580.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067190 restraints weight = 401.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067706 restraints weight = 323.648| |-----------------------------------------------------------------------------| r_work (final): 0.3090 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.054476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.053748 restraints weight = 300.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.054041 restraints weight = 42.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.054202 restraints weight = 20.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.054236 restraints weight = 12.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.054236 restraints weight = 10.576| |-----------------------------------------------------------------------------| r_work (final): 0.2521 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116221 restraints weight = 270.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116937 restraints weight = 129.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117513 restraints weight = 83.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117773 restraints weight = 60.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118023 restraints weight = 49.373| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.499 16392 Z= 0.508 Angle : 1.245 43.136 22440 Z= 0.516 Chirality : 0.056 0.397 2754 Planarity : 0.006 0.109 2685 Dihedral : 5.986 35.686 1962 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.41 (0.19), residues: 1800 helix: 0.42 (0.25), residues: 393 sheet: -0.05 (0.24), residues: 408 loop : -0.59 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 166 TYR 0.023 0.002 TYR I 110 PHE 0.015 0.002 PHE E 376 TRP 0.033 0.002 TRP C 427 HIS 0.010 0.002 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (16245) covalent geometry : angle 0.90269 / 0.43 (22038) SS BOND : bond 0.00284 / 0.18 ( 39) SS BOND : angle 1.39011 / 0.90 ( 78) hydrogen bonds : bond 0.05881 / 3.88 ( 588) hydrogen bonds : angle 5.06184 / 3.50 ( 1881) link_ALPHA1-3 : bond 0.48914 / 24.52 ( 3) link_ALPHA1-3 : angle 15.95205 / 10.69 ( 9) link_ALPHA1-6 : bond 0.49935 / 25.03 ( 3) link_ALPHA1-6 : angle 33.53851 / 20.69 ( 9) link_BETA1-4 : bond 0.00466 / 0.28 ( 36) link_BETA1-4 : angle 2.16665 / 1.63 ( 108) link_NAG-ASN : bond 0.00667 / 0.41 ( 66) link_NAG-ASN : angle 4.33999 / 2.84 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: C 104 MET cc_start: 0.9024 (tpp) cc_final: 0.8734 (tpp) REVERT: C 112 TRP cc_start: 0.8830 (t-100) cc_final: 0.8070 (t-100) REVERT: C 140 ASP cc_start: 0.8505 (m-30) cc_final: 0.8222 (m-30) REVERT: C 195 ASN cc_start: 0.8188 (m-40) cc_final: 0.7938 (m-40) REVERT: C 244 THR cc_start: 0.9116 (m) cc_final: 0.8657 (p) REVERT: C 426 MET cc_start: 0.8614 (ttm) cc_final: 0.8370 (ttm) REVERT: C 434 MET cc_start: 0.8593 (ttm) cc_final: 0.7266 (mtm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0339 time to fit residues: 3.0047 Evaluate side-chains 45 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.135 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.043 Fit side-chains REVERT: F 522 PHE cc_start: 0.7849 (t80) cc_final: 0.7360 (t80) REVERT: F 588 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8415 (mmm-85) REVERT: F 626 MET cc_start: 0.7692 (mtm) cc_final: 0.7226 (mtm) REVERT: F 633 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9222 (tppt) REVERT: F 634 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8542 (tp30) REVERT: F 654 GLU cc_start: 0.9193 (tp30) cc_final: 0.8846 (tp30) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0613 time to fit residues: 1.9569 Evaluate side-chains 22 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.039 Evaluate side-chains 17 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.017 Fit side-chains revert: symmetry clash REVERT: G 142 TYR cc_start: 0.7602 (m-80) cc_final: 0.7158 (m-80) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0489 time to fit residues: 0.8888 Evaluate side-chains 13 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.016 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067761 restraints weight = 11767.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069919 restraints weight = 6412.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071545 restraints weight = 4101.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.072647 restraints weight = 2859.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073509 restraints weight = 2161.299| |-----------------------------------------------------------------------------| r_work (final): 0.3050 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061193 restraints weight = 4825.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062756 restraints weight = 2807.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.063843 restraints weight = 1913.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064546 restraints weight = 1450.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065098 restraints weight = 1199.384| |-----------------------------------------------------------------------------| r_work (final): 0.3067 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062969 restraints weight = 1770.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064639 restraints weight = 750.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065653 restraints weight = 404.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066330 restraints weight = 254.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066558 restraints weight = 181.742| |-----------------------------------------------------------------------------| r_work (final): 0.3100 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.054522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.053734 restraints weight = 237.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.054053 restraints weight = 40.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.054212 restraints weight = 20.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.054313 restraints weight = 12.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.054374 restraints weight = 8.541 | |-----------------------------------------------------------------------------| r_work (final): 0.2516 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115383 restraints weight = 280.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116144 restraints weight = 135.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116618 restraints weight = 88.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116949 restraints weight = 65.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117207 restraints weight = 53.969| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.499 16392 Z= 0.508 Angle : 1.231 43.021 22440 Z= 0.514 Chirality : 0.055 0.394 2754 Planarity : 0.005 0.081 2685 Dihedral : 5.867 34.956 1962 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.54 (0.19), residues: 1800 helix: 0.19 (0.24), residues: 411 sheet: -0.01 (0.25), residues: 393 loop : -0.69 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 166 TYR 0.022 0.002 TYR H 142 PHE 0.029 0.002 PHE I 130 TRP 0.015 0.002 TRP A 427 HIS 0.014 0.002 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16245) covalent geometry : angle 0.89041 / 0.43 (22038) SS BOND : bond 0.00347 / 0.20 ( 39) SS BOND : angle 1.41402 / 0.92 ( 78) hydrogen bonds : bond 0.05407 / 3.56 ( 588) hydrogen bonds : angle 5.01893 / 3.49 ( 1881) link_ALPHA1-3 : bond 0.48389 / 24.25 ( 3) link_ALPHA1-3 : angle 15.72737 / 10.54 ( 9) link_ALPHA1-6 : bond 0.49892 / 25.01 ( 3) link_ALPHA1-6 : angle 33.43743 / 20.63 ( 9) link_BETA1-4 : bond 0.00438 / 0.26 ( 36) link_BETA1-4 : angle 2.12991 / 1.60 ( 108) link_NAG-ASN : bond 0.00583 / 0.35 ( 66) link_NAG-ASN : angle 4.27132 / 2.79 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: C 104 MET cc_start: 0.8981 (tpp) cc_final: 0.8720 (tpp) REVERT: C 112 TRP cc_start: 0.8837 (t-100) cc_final: 0.8113 (t-100) REVERT: C 140 ASP cc_start: 0.8516 (m-30) cc_final: 0.8232 (m-30) REVERT: C 164 GLU cc_start: 0.8788 (pm20) cc_final: 0.8281 (tt0) REVERT: C 195 ASN cc_start: 0.8154 (m-40) cc_final: 0.7932 (m-40) REVERT: C 244 THR cc_start: 0.9129 (m) cc_final: 0.8669 (p) REVERT: C 426 MET cc_start: 0.8869 (ttm) cc_final: 0.8388 (ttm) REVERT: C 434 MET cc_start: 0.8677 (ttm) cc_final: 0.7412 (mtm) REVERT: C 450 THR cc_start: 0.8530 (p) cc_final: 0.7795 (t) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0419 time to fit residues: 3.5604 Evaluate side-chains 45 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.138 Evaluate side-chains 25 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 Fit side-chains REVERT: F 522 PHE cc_start: 0.7869 (t80) cc_final: 0.7344 (t80) REVERT: F 589 ASP cc_start: 0.9045 (m-30) cc_final: 0.8628 (m-30) REVERT: F 626 MET cc_start: 0.7588 (mtm) cc_final: 0.7138 (mtp) REVERT: F 633 LYS cc_start: 0.9505 (mmmm) cc_final: 0.9231 (tppt) REVERT: F 634 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8631 (tp30) REVERT: F 654 GLU cc_start: 0.9258 (tp30) cc_final: 0.8885 (tp30) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0515 time to fit residues: 1.4502 Evaluate side-chains 19 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.038 Evaluate side-chains 16 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.017 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0367 time to fit residues: 0.6446 Evaluate side-chains 14 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 60 optimal weight: 0.0040 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 137 optimal weight: 0.0000 chunk 94 optimal weight: 0.0970 chunk 102 optimal weight: 0.0270 chunk 162 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 71 optimal weight: 0.0040 chunk 16 optimal weight: 0.7980 overall best weight: 0.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.068855 restraints weight = 11429.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.071113 restraints weight = 6214.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.072757 restraints weight = 3932.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073907 restraints weight = 2733.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074770 restraints weight = 2057.667| |-----------------------------------------------------------------------------| r_work (final): 0.3070 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.072919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061912 restraints weight = 4986.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063495 restraints weight = 2833.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064571 restraints weight = 1908.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.065270 restraints weight = 1446.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065800 restraints weight = 1199.919| |-----------------------------------------------------------------------------| r_work (final): 0.3084 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.063494 restraints weight = 1829.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.065120 restraints weight = 801.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066069 restraints weight = 442.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066791 restraints weight = 287.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066986 restraints weight = 205.388| |-----------------------------------------------------------------------------| r_work (final): 0.3108 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.045130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.044928 restraints weight = 174.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.045046 restraints weight = 12.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.045045 restraints weight = 1.499 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.045045 restraints weight = 0.247 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.045045 restraints weight = 0.247 | |-----------------------------------------------------------------------------| r_work (final): 0.2446 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118154 restraints weight = 243.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118850 restraints weight = 123.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119216 restraints weight = 81.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119573 restraints weight = 62.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119769 restraints weight = 48.920| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.499 16392 Z= 0.498 Angle : 1.204 42.889 22440 Z= 0.496 Chirality : 0.055 0.396 2754 Planarity : 0.005 0.079 2685 Dihedral : 5.797 34.317 1962 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.54 (0.19), residues: 1800 helix: 0.35 (0.25), residues: 411 sheet: -0.20 (0.25), residues: 414 loop : -0.68 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 166 TYR 0.019 0.002 TYR H 142 PHE 0.017 0.002 PHE E 376 TRP 0.016 0.002 TRP C 69 HIS 0.010 0.001 HIS E 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16245) covalent geometry : angle 0.86149 / 0.41 (22038) SS BOND : bond 0.00716 / 0.43 ( 39) SS BOND : angle 1.27840 / 0.83 ( 78) hydrogen bonds : bond 0.05216 / 3.41 ( 588) hydrogen bonds : angle 5.02740 / 3.47 ( 1881) link_ALPHA1-3 : bond 0.48407 / 24.26 ( 3) link_ALPHA1-3 : angle 15.62103 / 10.47 ( 9) link_ALPHA1-6 : bond 0.49914 / 25.02 ( 3) link_ALPHA1-6 : angle 33.40538 / 20.61 ( 9) link_BETA1-4 : bond 0.00437 / 0.26 ( 36) link_BETA1-4 : angle 2.04191 / 1.55 ( 108) link_NAG-ASN : bond 0.00665 / 0.40 ( 66) link_NAG-ASN : angle 4.11884 / 2.70 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: C 93 PHE cc_start: 0.7274 (m-80) cc_final: 0.6930 (m-80) REVERT: C 112 TRP cc_start: 0.8858 (t-100) cc_final: 0.8071 (t-100) REVERT: C 116 LEU cc_start: 0.9503 (mp) cc_final: 0.9013 (mp) REVERT: C 140 ASP cc_start: 0.8400 (m-30) cc_final: 0.8136 (m-30) REVERT: C 164 GLU cc_start: 0.8722 (pm20) cc_final: 0.8297 (tt0) REVERT: C 244 THR cc_start: 0.9135 (m) cc_final: 0.8671 (p) REVERT: C 426 MET cc_start: 0.8811 (ttm) cc_final: 0.8232 (ttm) REVERT: C 434 MET cc_start: 0.8586 (ttm) cc_final: 0.7347 (mtm) REVERT: C 450 THR cc_start: 0.8550 (p) cc_final: 0.7858 (t) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0362 time to fit residues: 3.3025 Evaluate side-chains 47 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.139 Evaluate side-chains 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.040 Fit side-chains REVERT: F 522 PHE cc_start: 0.7847 (t80) cc_final: 0.7297 (t80) REVERT: F 626 MET cc_start: 0.7651 (mtm) cc_final: 0.7354 (mtp) REVERT: F 633 LYS cc_start: 0.9516 (mmmm) cc_final: 0.9216 (tppt) REVERT: F 634 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8582 (tp30) REVERT: F 654 GLU cc_start: 0.9328 (tp30) cc_final: 0.8863 (tp30) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0501 time to fit residues: 1.4733 Evaluate side-chains 18 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.038 Evaluate side-chains 15 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0376 time to fit residues: 0.6195 Evaluate side-chains 12 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 60 optimal weight: 0.7980 chunk 165 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 147 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 352 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.068175 restraints weight = 11549.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070368 restraints weight = 6335.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.071961 restraints weight = 4043.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073149 restraints weight = 2823.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073966 restraints weight = 2110.329| |-----------------------------------------------------------------------------| r_work (final): 0.3058 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060048 restraints weight = 4696.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.061632 restraints weight = 2695.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.062723 restraints weight = 1833.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.063425 restraints weight = 1387.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.063666 restraints weight = 1149.088| |-----------------------------------------------------------------------------| r_work (final): 0.3064 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.061499 restraints weight = 1768.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.063003 restraints weight = 822.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064012 restraints weight = 479.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064725 restraints weight = 315.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064726 restraints weight = 224.839| |-----------------------------------------------------------------------------| r_work (final): 0.3054 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.050803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.050515 restraints weight = 214.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.050582 restraints weight = 10.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.050597 restraints weight = 1.298 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.050584 restraints weight = 0.252 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.050583 restraints weight = 0.050 | |-----------------------------------------------------------------------------| r_work (final): 0.2523 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116404 restraints weight = 301.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117036 restraints weight = 142.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117514 restraints weight = 94.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117828 restraints weight = 69.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117828 restraints weight = 56.491| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.499 16392 Z= 0.500 Angle : 1.178 42.923 22440 Z= 0.484 Chirality : 0.053 0.386 2754 Planarity : 0.005 0.070 2685 Dihedral : 5.645 32.812 1962 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1800 helix: 0.54 (0.25), residues: 411 sheet: -0.11 (0.24), residues: 447 loop : -0.70 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.030 0.002 TYR I 142 PHE 0.012 0.001 PHE C 376 TRP 0.024 0.002 TRP A 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16245) covalent geometry : angle 0.82780 / 0.40 (22038) SS BOND : bond 0.00347 / 0.23 ( 39) SS BOND : angle 1.20751 / 0.77 ( 78) hydrogen bonds : bond 0.04918 / 3.21 ( 588) hydrogen bonds : angle 4.98073 / 3.44 ( 1881) link_ALPHA1-3 : bond 0.48344 / 24.23 ( 3) link_ALPHA1-3 : angle 15.31701 / 10.26 ( 9) link_ALPHA1-6 : bond 0.49911 / 25.02 ( 3) link_ALPHA1-6 : angle 33.38991 / 20.60 ( 9) link_BETA1-4 : bond 0.00370 / 0.22 ( 36) link_BETA1-4 : angle 2.04152 / 1.53 ( 108) link_NAG-ASN : bond 0.00502 / 0.29 ( 66) link_NAG-ASN : angle 4.08955 / 2.68 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: C 93 PHE cc_start: 0.7275 (m-80) cc_final: 0.6870 (m-80) REVERT: C 112 TRP cc_start: 0.8858 (t-100) cc_final: 0.8098 (t-100) REVERT: C 116 LEU cc_start: 0.9497 (mp) cc_final: 0.9124 (mt) REVERT: C 140 ASP cc_start: 0.8417 (m-30) cc_final: 0.8153 (m-30) REVERT: C 164 GLU cc_start: 0.8703 (pm20) cc_final: 0.8382 (tt0) REVERT: C 244 THR cc_start: 0.9130 (m) cc_final: 0.8680 (p) REVERT: C 352 HIS cc_start: 0.8823 (t70) cc_final: 0.8622 (t70) REVERT: C 426 MET cc_start: 0.8767 (ttm) cc_final: 0.8257 (ttm) REVERT: C 434 MET cc_start: 0.8624 (ttm) cc_final: 0.7376 (mtm) REVERT: C 450 THR cc_start: 0.8554 (p) cc_final: 0.7933 (t) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0363 time to fit residues: 3.2624 Evaluate side-chains 51 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.140 Evaluate side-chains 24 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.039 Fit side-chains REVERT: B 522 PHE cc_start: 0.7722 (t80) cc_final: 0.7222 (t80) REVERT: B 626 MET cc_start: 0.8139 (mtm) cc_final: 0.7615 (mtm) REVERT: B 633 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9137 (tppt) REVERT: B 634 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8523 (tp30) REVERT: B 654 GLU cc_start: 0.9196 (tp30) cc_final: 0.8793 (tp30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0521 time to fit residues: 1.4135 Evaluate side-chains 17 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.042 Evaluate side-chains 16 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.017 Fit side-chains revert: symmetry clash REVERT: G 102 LYS cc_start: 0.7595 (tttt) cc_final: 0.7132 (tptt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0343 time to fit residues: 0.6046 Evaluate side-chains 12 residues out of total 44 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 135 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 168 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.068042 restraints weight = 11614.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.070127 restraints weight = 6325.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.071696 restraints weight = 4099.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072853 restraints weight = 2860.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.073712 restraints weight = 2153.039| |-----------------------------------------------------------------------------| r_work (final): 0.3057 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.060790 restraints weight = 4778.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.062549 restraints weight = 2680.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.063691 restraints weight = 1775.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064493 restraints weight = 1323.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065000 restraints weight = 1059.299| |-----------------------------------------------------------------------------| r_work (final): 0.3091 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.067652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.061049 restraints weight = 1752.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062627 restraints weight = 802.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.063541 restraints weight = 459.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064141 restraints weight = 307.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064341 restraints weight = 232.177| |-----------------------------------------------------------------------------| r_work (final): 0.3063 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.044199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.044070 restraints weight = 182.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.044125 restraints weight = 9.484 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.044137 restraints weight = 1.384 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.044139 restraints weight = 0.202 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.044139 restraints weight = 0.112 | |-----------------------------------------------------------------------------| r_work (final): 0.2425 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116842 restraints weight = 253.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117537 restraints weight = 127.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117935 restraints weight = 86.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.118303 restraints weight = 68.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118543 restraints weight = 54.667| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.499 16392 Z= 0.499 Angle : 1.214 42.858 22440 Z= 0.496 Chirality : 0.054 0.395 2754 Planarity : 0.005 0.068 2685 Dihedral : 5.672 32.239 1962 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.41 (0.19), residues: 1800 helix: 0.59 (0.25), residues: 411 sheet: -0.08 (0.24), residues: 447 loop : -0.70 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 166 TYR 0.022 0.002 TYR I 142 PHE 0.024 0.002 PHE I 130 TRP 0.017 0.002 TRP A 479 HIS 0.014 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16245) covalent geometry : angle 0.84626 / 0.40 (22038) SS BOND : bond 0.00312 / 0.20 ( 39) SS BOND : angle 1.13314 / 0.73 ( 78) hydrogen bonds : bond 0.05018 / 3.17 ( 588) hydrogen bonds : angle 4.81586 / 3.32 ( 1881) link_ALPHA1-3 : bond 0.48210 / 24.17 ( 3) link_ALPHA1-3 : angle 15.14688 / 10.15 ( 9) link_ALPHA1-6 : bond 0.49863 / 24.99 ( 3) link_ALPHA1-6 : angle 33.36453 / 20.59 ( 9) link_BETA1-4 : bond 0.00279 / 0.15 ( 36) link_BETA1-4 : angle 1.96341 / 1.47 ( 108) link_NAG-ASN : bond 0.00541 / 0.33 ( 66) link_NAG-ASN : angle 4.85339 / 3.22 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.38 seconds wall clock time: 32 minutes 59.55 seconds (1979.55 seconds total)