Starting phenix.real_space_refine on Sat Sep 12 10:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.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 { model { file = "/net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vl5_21230/09_2026/6vl5_21230.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= 0.001 sd= 0.005 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 99 5.16 5 C 9378 2.51 5 N 2478 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 15039 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "D" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "F" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.16, per 1000 atoms: 0.21 Number of scatterers: 15039 At special positions: 0 Unit cell: (126.5, 127.65, 117.3, 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 99 16.00 O 3084 8.00 N 2478 7.00 C 9378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.10 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 608 " - " ASN A 160 " " NAG A 609 " - " ASN A 276 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 363 " " NAG A 618 " - " ASN A 133 " " NAG A 627 " - " ASN A 289 " " NAG A 630 " - " ASN A 339 " " NAG A 631 " - " ASN A 355 " " NAG A 632 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 276 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 363 " " NAG C 618 " - " ASN C 133 " " NAG C 627 " - " ASN C 289 " " NAG C 630 " - " ASN C 339 " " NAG C 631 " - " ASN C 355 " " NAG C 632 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 276 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 363 " " NAG E 618 " - " ASN E 133 " " NAG E 627 " - " ASN E 289 " " NAG E 630 " - " ASN E 339 " " NAG E 631 " - " ASN E 355 " " NAG E 632 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG H 1 " - " ASN C 448 " " NAG I 1 " - " ASN C 295 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 197 " " NAG L 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 88 " " NAG O 1 " - " ASN C 241 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 88 " " NAG Y 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " " NAG c 1 " - " ASN E 295 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 241 " " NAG j 1 " - " ASN E 332 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 557.1 milliseconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 29.1% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.519A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.537A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 543 through 544 No H-bonds generated for 'chain 'D' and resid 543 through 544' Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) 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 661 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.518A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.537A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 544 No H-bonds generated for 'chain 'B' and resid 543 through 544' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) 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 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.520A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.536A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 543 through 544 No H-bonds generated for 'chain 'F' and resid 543 through 544' Processing helix chain 'F' and resid 545 through 549 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) 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 661 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.406A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.840A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.479A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 4.045A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.491A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.934A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 394 through 396 removed outlier: 6.377A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.841A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.046A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.492A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.933A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 394 through 396 removed outlier: 6.377A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.404A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.840A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.046A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.492A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.933A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 394 through 396 removed outlier: 6.378A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3278 1.32 - 1.45: 4445 1.45 - 1.58: 7459 1.58 - 1.71: 4 1.71 - 1.84: 129 Bond restraints: 15315 Sorted by residual: bond pdb=" NE ARG E 308 " pdb=" CZ ARG E 308 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" CZ ARG C 503 " pdb=" NH2 ARG C 503 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" NE ARG A 308 " pdb=" CZ ARG A 308 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" CA ASN C 279 " pdb=" CB ASN C 279 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.27e-02 6.20e+03 1.24e+01 bond pdb=" CB HIS C 85 " pdb=" CG HIS C 85 " ideal model delta sigma weight residual 1.497 1.448 0.049 1.40e-02 5.10e+03 1.24e+01 ... (remaining 15310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 15250 1.67 - 3.33: 4231 3.33 - 5.00: 970 5.00 - 6.67: 284 6.67 - 8.34: 58 Bond angle restraints: 20793 Sorted by residual: angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.10 -8.23 1.04e+00 9.25e-01 6.26e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.04 -8.17 1.04e+00 9.25e-01 6.17e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.04 -8.17 1.04e+00 9.25e-01 6.17e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 107.84 99.50 8.34 1.11e+00 8.12e-01 5.64e+01 angle pdb=" N ILE E 213 " pdb=" CA ILE E 213 " pdb=" C ILE E 213 " ideal model delta sigma weight residual 107.84 99.53 8.31 1.11e+00 8.12e-01 5.61e+01 ... (remaining 20788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7996 17.65 - 35.29: 278 35.29 - 52.94: 63 52.94 - 70.58: 21 70.58 - 88.23: 9 Dihedral angle restraints: 8367 sinusoidal: 3402 harmonic: 4965 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.83 42.83 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.82 42.82 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.80 42.80 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 8364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1927 0.111 - 0.223: 651 0.223 - 0.334: 65 0.334 - 0.445: 12 0.445 - 0.557: 3 Chirality restraints: 2658 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.88e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.65e+01 ... (remaining 2655 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " -0.078 2.00e-02 2.50e+03 8.08e-02 8.16e+01 pdb=" CG ASN A 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG A 630 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.078 2.00e-02 2.50e+03 8.07e-02 8.15e+01 pdb=" CG ASN C 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG C 630 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " -0.078 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" CG ASN E 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG E 630 " -0.096 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3191 2.77 - 3.31: 13968 3.31 - 3.84: 25723 3.84 - 4.37: 30643 4.37 - 4.90: 48262 Nonbonded interactions: 121787 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.367 3.120 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.368 3.120 ... (remaining 121782 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 'Q' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints Number of NCS constrained groups: 4 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 'Q' selection = chain 'a' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 0.450 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.490 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.019 0.090 15453 Z= 1.006 Angle : 1.751 9.210 21174 Z= 1.093 Chirality : 0.104 0.557 2658 Planarity : 0.009 0.043 2499 Dihedral : 10.233 88.227 5052 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.20 % Allowed : 1.57 % Favored : 98.24 % 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: 0.88 (0.19), residues: 1683 helix: 0.15 (0.24), residues: 426 sheet: 1.08 (0.23), residues: 405 loop : 0.76 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 298 TYR 0.040 0.007 TYR E 319 PHE 0.031 0.006 PHE E 383 TRP 0.055 0.011 TRP A 479 HIS 0.010 0.002 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.01884 / 1.00 (15315) covalent geometry : angle 1.72480 / 1.09 (20793) SS BOND : bond 0.02664 / 1.73 ( 33) SS BOND : angle 1.88030 / 1.34 ( 66) hydrogen bonds : bond 0.15492 / 10.53 ( 555) hydrogen bonds : angle 7.37052 / 5.21 ( 1827) link_ALPHA1-3 : bond 0.03995 / 2.00 ( 3) link_ALPHA1-3 : angle 3.17604 / 2.17 ( 9) link_ALPHA1-6 : bond 0.03389 / 1.70 ( 3) link_ALPHA1-6 : angle 2.62673 / 1.74 ( 9) link_BETA1-4 : bond 0.03792 / 2.32 ( 33) link_BETA1-4 : angle 3.68898 / 2.52 ( 99) link_NAG-ASN : bond 0.02920 / 1.85 ( 66) link_NAG-ASN : angle 2.56024 / 1.83 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8423 (m-80) cc_final: 0.7822 (m-80) REVERT: A 40 TYR cc_start: 0.8768 (t80) cc_final: 0.7535 (p90) REVERT: A 49 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7493 (mm-30) REVERT: A 50 THR cc_start: 0.9322 (t) cc_final: 0.9082 (t) REVERT: A 63 THR cc_start: 0.6150 (p) cc_final: 0.5867 (p) REVERT: A 108 ILE cc_start: 0.9560 (mt) cc_final: 0.9269 (mt) REVERT: A 116 LEU cc_start: 0.9484 (tp) cc_final: 0.9273 (pp) REVERT: A 175 LEU cc_start: 0.8934 (mt) cc_final: 0.8459 (pt) REVERT: A 319 TYR cc_start: 0.8416 (p90) cc_final: 0.7949 (p90) REVERT: A 384 TYR cc_start: 0.9200 (m-80) cc_final: 0.8622 (m-80) REVERT: A 483 LEU cc_start: 0.9290 (mt) cc_final: 0.8952 (pp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0628 time to fit residues: 9.1924 Evaluate side-chains 58 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.148 Evaluate side-chains 70 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 540 GLN cc_start: 0.7994 (mm110) cc_final: 0.7777 (mt0) REVERT: B 544 LEU cc_start: 0.9276 (mm) cc_final: 0.8807 (mm) REVERT: B 545 LEU cc_start: 0.8971 (mt) cc_final: 0.8497 (pt) REVERT: B 575 GLN cc_start: 0.8881 (mt0) cc_final: 0.8366 (mp10) REVERT: B 576 LEU cc_start: 0.9072 (tp) cc_final: 0.8810 (tt) REVERT: B 579 ARG cc_start: 0.8577 (mtp180) cc_final: 0.7553 (ptt180) REVERT: B 610 TRP cc_start: 0.6697 (t-100) cc_final: 0.6097 (p90) REVERT: B 635 ILE cc_start: 0.9183 (pt) cc_final: 0.8874 (pt) REVERT: B 646 LEU cc_start: 0.9740 (mt) cc_final: 0.9479 (mm) REVERT: B 649 SER cc_start: 0.9433 (m) cc_final: 0.8632 (m) REVERT: B 650 GLN cc_start: 0.8766 (tp40) cc_final: 0.8137 (tm-30) REVERT: B 652 GLN cc_start: 0.8914 (mt0) cc_final: 0.8632 (mm-40) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.0637 time to fit residues: 4.8243 Evaluate side-chains 39 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.038 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: 0.0017 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: 0.0010 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: 168 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0270 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3264 r_free = 0.3264 target = 0.072610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061039 restraints weight = 14214.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063082 restraints weight = 8033.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064613 restraints weight = 5270.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065710 restraints weight = 3807.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066513 restraints weight = 2950.951| |-----------------------------------------------------------------------------| r_work (final): 0.3121 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.066899 restraints weight = 4421.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.068875 restraints weight = 2508.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070250 restraints weight = 1659.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071220 restraints weight = 1228.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071847 restraints weight = 990.023| |-----------------------------------------------------------------------------| r_work (final): 0.3175 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.060218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.053524 restraints weight = 366.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.054150 restraints weight = 155.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054462 restraints weight = 115.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054665 restraints weight = 100.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054664 restraints weight = 92.724| |-----------------------------------------------------------------------------| r_work (final): 0.2731 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2109 r_free = 0.2109 target = 0.034855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2118 r_free = 0.2118 target = 0.034513 restraints weight = 171.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2108 r_free = 0.2108 target = 0.034753 restraints weight = 18.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2108 r_free = 0.2108 target = 0.034853 restraints weight = 3.517 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2108 r_free = 0.2108 target = 0.034866 restraints weight = 0.730 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2107 r_free = 0.2107 target = 0.034855 restraints weight = 0.156 | |-----------------------------------------------------------------------------| r_work (final): 0.2141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 15453 Z= 0.307 Angle : 1.246 30.207 21174 Z= 0.597 Chirality : 0.057 0.323 2658 Planarity : 0.008 0.125 2499 Dihedral : 5.998 30.118 1818 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.59 % Allowed : 3.33 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1683 helix: 0.39 (0.25), residues: 390 sheet: 0.62 (0.22), residues: 465 loop : -0.13 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 298 TYR 0.026 0.004 TYR E 39 PHE 0.022 0.003 PHE F 522 TRP 0.036 0.004 TRP C 96 HIS 0.017 0.004 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.30 (15315) covalent geometry : angle 1.01509 / 0.54 (20793) SS BOND : bond 0.00819 / 0.46 ( 33) SS BOND : angle 3.71133 / 2.44 ( 66) hydrogen bonds : bond 0.09426 / 6.29 ( 555) hydrogen bonds : angle 5.95740 / 4.22 ( 1827) link_ALPHA1-3 : bond 0.00885 / 0.44 ( 3) link_ALPHA1-3 : angle 2.00410 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00488 / 0.24 ( 3) link_ALPHA1-6 : angle 1.29673 / 0.75 ( 9) link_BETA1-4 : bond 0.00638 / 0.38 ( 33) link_BETA1-4 : angle 1.73842 / 1.17 ( 99) link_NAG-ASN : bond 0.01243 / 0.88 ( 66) link_NAG-ASN : angle 7.17167 / 5.42 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8573 (m-80) cc_final: 0.8186 (m-80) REVERT: A 86 LEU cc_start: 0.9233 (mm) cc_final: 0.8990 (mm) REVERT: A 95 MET cc_start: 0.8560 (ppp) cc_final: 0.8255 (ppp) REVERT: A 98 ASN cc_start: 0.9193 (t0) cc_final: 0.8873 (t0) REVERT: A 104 MET cc_start: 0.8882 (mmm) cc_final: 0.8604 (tpp) REVERT: A 127 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 288 LEU cc_start: 0.9182 (mt) cc_final: 0.8863 (mp) REVERT: A 308 ARG cc_start: 0.8203 (ttm110) cc_final: 0.7833 (ttt180) REVERT: A 483 LEU cc_start: 0.9096 (mt) cc_final: 0.8645 (mt) outliers start: 2 outliers final: 0 residues processed: 73 average time/residue: 0.0666 time to fit residues: 6.1073 Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.142 Evaluate side-chains 53 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 523 LEU cc_start: 0.8731 (mp) cc_final: 0.8490 (mp) REVERT: F 536 THR cc_start: 0.8330 (t) cc_final: 0.8019 (t) REVERT: F 539 VAL cc_start: 0.8999 (t) cc_final: 0.8280 (p) REVERT: F 575 GLN cc_start: 0.8577 (mt0) cc_final: 0.8287 (mt0) REVERT: F 576 LEU cc_start: 0.8938 (tp) cc_final: 0.8537 (tt) REVERT: F 579 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7472 (ptt180) REVERT: F 628 TRP cc_start: 0.7520 (m-10) cc_final: 0.5538 (p-90) REVERT: F 643 TYR cc_start: 0.8563 (m-10) cc_final: 0.8266 (m-10) REVERT: F 649 SER cc_start: 0.9235 (m) cc_final: 0.8367 (m) REVERT: F 651 ASN cc_start: 0.8958 (t0) cc_final: 0.8737 (t0) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0590 time to fit residues: 3.3550 Evaluate side-chains 37 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.039 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: 0.0017 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: 0.0009 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 166 optimal weight: 0.0470 chunk 135 optimal weight: 7.9990 chunk 158 optimal weight: 0.5980 chunk 94 optimal weight: 0.0470 chunk 107 optimal weight: 0.0980 chunk 53 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 10 optimal weight: 0.0050 chunk 152 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.060280 restraints weight = 14227.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.062335 restraints weight = 8063.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063844 restraints weight = 5306.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064842 restraints weight = 3846.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065613 restraints weight = 3021.785| |-----------------------------------------------------------------------------| r_work (final): 0.3090 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.082436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068267 restraints weight = 4423.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070135 restraints weight = 2466.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071386 restraints weight = 1640.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072267 restraints weight = 1224.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072798 restraints weight = 1005.465| |-----------------------------------------------------------------------------| r_work (final): 0.3179 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.056999 restraints weight = 345.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.057568 restraints weight = 277.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.058013 restraints weight = 244.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.058021 restraints weight = 221.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.058021 restraints weight = 220.510| |-----------------------------------------------------------------------------| r_work (final): 0.2760 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.038392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2247 r_free = 0.2247 target = 0.037800 restraints weight = 143.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.038160 restraints weight = 23.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.038352 restraints weight = 5.305 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.038354 restraints weight = 1.467 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.038354 restraints weight = 0.437 | |-----------------------------------------------------------------------------| r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 15453 Z= 0.288 Angle : 1.137 28.710 21174 Z= 0.545 Chirality : 0.055 0.314 2658 Planarity : 0.006 0.046 2499 Dihedral : 6.261 37.118 1818 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.78 % Allowed : 3.91 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: 0.03 (0.20), residues: 1683 helix: 0.71 (0.26), residues: 375 sheet: 0.25 (0.22), residues: 471 loop : -0.34 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 298 TYR 0.026 0.003 TYR A 39 PHE 0.018 0.002 PHE D 522 TRP 0.046 0.004 TRP E 96 HIS 0.012 0.003 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.29 (15315) covalent geometry : angle 0.96054 / 0.51 (20793) SS BOND : bond 0.00703 / 0.41 ( 33) SS BOND : angle 2.35725 / 1.60 ( 66) hydrogen bonds : bond 0.08138 / 5.40 ( 555) hydrogen bonds : angle 5.87716 / 4.15 ( 1827) link_ALPHA1-3 : bond 0.00619 / 0.31 ( 3) link_ALPHA1-3 : angle 1.48393 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00109 / 0.05 ( 3) link_ALPHA1-6 : angle 1.47498 / 0.90 ( 9) link_BETA1-4 : bond 0.00503 / 0.30 ( 33) link_BETA1-4 : angle 1.49314 / 1.01 ( 99) link_NAG-ASN : bond 0.01045 / 0.67 ( 66) link_NAG-ASN : angle 6.17856 / 4.71 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8401 (m-80) cc_final: 0.8148 (m-80) REVERT: A 40 TYR cc_start: 0.8696 (t80) cc_final: 0.7725 (p90) REVERT: A 69 TRP cc_start: 0.8856 (m100) cc_final: 0.8560 (m100) REVERT: A 86 LEU cc_start: 0.9173 (mm) cc_final: 0.8909 (mm) REVERT: A 95 MET cc_start: 0.8531 (ppp) cc_final: 0.8069 (ppp) REVERT: A 98 ASN cc_start: 0.9268 (t0) cc_final: 0.8821 (t0) REVERT: A 104 MET cc_start: 0.8911 (mmm) cc_final: 0.8585 (tpp) REVERT: A 288 LEU cc_start: 0.9134 (mt) cc_final: 0.8924 (mp) REVERT: A 384 TYR cc_start: 0.9178 (m-80) cc_final: 0.8935 (m-10) outliers start: 3 outliers final: 0 residues processed: 71 average time/residue: 0.0637 time to fit residues: 5.7161 Evaluate side-chains 53 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.148 Evaluate side-chains 50 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 536 THR cc_start: 0.8364 (t) cc_final: 0.8151 (t) REVERT: F 539 VAL cc_start: 0.8898 (t) cc_final: 0.8659 (m) REVERT: F 575 GLN cc_start: 0.8522 (mt0) cc_final: 0.8246 (mt0) REVERT: F 576 LEU cc_start: 0.8723 (tp) cc_final: 0.8369 (tt) REVERT: F 579 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7325 (ptt180) REVERT: F 628 TRP cc_start: 0.7579 (m-10) cc_final: 0.5691 (p-90) REVERT: F 653 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8036 (tm-30) outliers start: 1 outliers final: 0 residues processed: 50 average time/residue: 0.0486 time to fit residues: 2.6842 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.039 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 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: 0.0010 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: 168 random chunks: chunk 156 optimal weight: 10.0000 chunk 67 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 overall best weight: 4.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.059991 restraints weight = 14826.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061957 restraints weight = 8177.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063402 restraints weight = 5311.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064417 restraints weight = 3840.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.065004 restraints weight = 2992.381| |-----------------------------------------------------------------------------| r_work (final): 0.3049 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.081483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067268 restraints weight = 4588.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068967 restraints weight = 2706.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070123 restraints weight = 1839.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070923 restraints weight = 1407.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071512 restraints weight = 1170.655| |-----------------------------------------------------------------------------| r_work (final): 0.3147 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.061818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.055733 restraints weight = 382.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.056317 restraints weight = 309.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.056764 restraints weight = 268.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.057161 restraints weight = 245.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057418 restraints weight = 224.838| |-----------------------------------------------------------------------------| r_work (final): 0.2740 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2215 r_free = 0.2215 target = 0.037025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2219 r_free = 0.2219 target = 0.036905 restraints weight = 153.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2217 r_free = 0.2217 target = 0.037032 restraints weight = 10.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.037035 restraints weight = 1.044 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.037035 restraints weight = 0.242 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.037035 restraints weight = 0.242 | |-----------------------------------------------------------------------------| r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 15453 Z= 0.305 Angle : 1.078 26.196 21174 Z= 0.520 Chirality : 0.054 0.281 2658 Planarity : 0.006 0.075 2499 Dihedral : 6.235 32.133 1818 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.59 % Allowed : 1.37 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: 0.07 (0.20), residues: 1683 helix: 0.78 (0.26), residues: 375 sheet: 0.38 (0.22), residues: 492 loop : -0.43 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.002 ARG A 166 TYR 0.015 0.003 TYR C 39 PHE 0.015 0.002 PHE F 522 TRP 0.104 0.006 TRP B 610 HIS 0.020 0.003 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.30 (15315) covalent geometry : angle 0.93211 / 0.49 (20793) SS BOND : bond 0.00587 / 0.34 ( 33) SS BOND : angle 2.06264 / 1.38 ( 66) hydrogen bonds : bond 0.07585 / 5.08 ( 555) hydrogen bonds : angle 5.83325 / 4.09 ( 1827) link_ALPHA1-3 : bond 0.00688 / 0.34 ( 3) link_ALPHA1-3 : angle 1.14092 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00528 / 0.26 ( 3) link_ALPHA1-6 : angle 1.24304 / 0.83 ( 9) link_BETA1-4 : bond 0.00623 / 0.38 ( 33) link_BETA1-4 : angle 1.56836 / 1.08 ( 99) link_NAG-ASN : bond 0.00936 / 0.61 ( 66) link_NAG-ASN : angle 5.50321 / 4.20 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.145 Fit side-chains REVERT: C 39 TYR cc_start: 0.8388 (m-10) cc_final: 0.8183 (m-80) REVERT: C 40 TYR cc_start: 0.8561 (t80) cc_final: 0.7731 (p90) REVERT: C 86 LEU cc_start: 0.9065 (mm) cc_final: 0.8683 (mm) REVERT: C 95 MET cc_start: 0.8586 (ppp) cc_final: 0.8229 (ppp) REVERT: C 98 ASN cc_start: 0.9341 (t0) cc_final: 0.8974 (t0) REVERT: C 104 MET cc_start: 0.9030 (mmm) cc_final: 0.8789 (tpp) REVERT: C 426 MET cc_start: 0.8041 (ttp) cc_final: 0.5313 (ttp) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.0619 time to fit residues: 4.7073 Evaluate side-chains 45 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.238 Evaluate side-chains 40 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 575 GLN cc_start: 0.8455 (mt0) cc_final: 0.8027 (mt0) REVERT: D 589 ASP cc_start: 0.8677 (m-30) cc_final: 0.8320 (m-30) REVERT: D 622 ILE cc_start: 0.8214 (mt) cc_final: 0.7802 (mm) REVERT: D 626 MET cc_start: 0.7962 (mtt) cc_final: 0.7583 (mtt) REVERT: D 647 GLU cc_start: 0.8864 (pt0) cc_final: 0.8531 (tp30) REVERT: D 653 GLN cc_start: 0.9068 (tm-30) cc_final: 0.7953 (tm-30) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.0494 time to fit residues: 2.1540 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.039 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 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 : 0.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 122 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 158 optimal weight: 0.0030 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 0.3980 chunk 97 optimal weight: 0.0000 chunk 149 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 109 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059806 restraints weight = 14763.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061857 restraints weight = 8320.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063335 restraints weight = 5494.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064417 restraints weight = 4007.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065188 restraints weight = 3142.297| |-----------------------------------------------------------------------------| r_work (final): 0.3069 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065909 restraints weight = 4480.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.067616 restraints weight = 2601.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068810 restraints weight = 1746.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069630 restraints weight = 1302.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070111 restraints weight = 1064.688| |-----------------------------------------------------------------------------| r_work (final): 0.3147 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.061581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.055945 restraints weight = 372.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.056488 restraints weight = 308.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.056878 restraints weight = 271.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.056878 restraints weight = 246.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.056878 restraints weight = 246.255| |-----------------------------------------------------------------------------| r_work (final): 0.2725 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.034652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2140 r_free = 0.2140 target = 0.034531 restraints weight = 196.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2141 r_free = 0.2141 target = 0.034599 restraints weight = 11.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2142 r_free = 0.2142 target = 0.034637 restraints weight = 1.257 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2142 r_free = 0.2142 target = 0.034624 restraints weight = 0.141 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2142 r_free = 0.2142 target = 0.034624 restraints weight = 0.017 | |-----------------------------------------------------------------------------| r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15453 Z= 0.211 Angle : 1.002 23.342 21174 Z= 0.473 Chirality : 0.056 0.429 2658 Planarity : 0.006 0.072 2499 Dihedral : 6.119 34.903 1818 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.20), residues: 1683 helix: 0.62 (0.25), residues: 390 sheet: 0.24 (0.23), residues: 471 loop : -0.61 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 166 TYR 0.016 0.002 TYR A 319 PHE 0.013 0.002 PHE B 522 TRP 0.076 0.005 TRP A 96 HIS 0.018 0.003 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (15315) covalent geometry : angle 0.88477 / 0.45 (20793) SS BOND : bond 0.01342 / 0.84 ( 33) SS BOND : angle 1.62632 / 1.08 ( 66) hydrogen bonds : bond 0.06591 / 4.41 ( 555) hydrogen bonds : angle 5.71998 / 4.03 ( 1827) link_ALPHA1-3 : bond 0.00713 / 0.36 ( 3) link_ALPHA1-3 : angle 1.22640 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00495 / 0.25 ( 3) link_ALPHA1-6 : angle 1.30481 / 0.88 ( 9) link_BETA1-4 : bond 0.00423 / 0.26 ( 33) link_BETA1-4 : angle 1.40309 / 0.97 ( 99) link_NAG-ASN : bond 0.00592 / 0.41 ( 66) link_NAG-ASN : angle 4.81628 / 3.67 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.119 Fit side-chains REVERT: A 39 TYR cc_start: 0.8214 (m-10) cc_final: 0.7983 (m-10) REVERT: A 86 LEU cc_start: 0.9127 (mm) cc_final: 0.8789 (mm) REVERT: A 95 MET cc_start: 0.8360 (ppp) cc_final: 0.7921 (ppp) REVERT: A 98 ASN cc_start: 0.9287 (t0) cc_final: 0.8913 (t0) REVERT: A 104 MET cc_start: 0.9068 (mmm) cc_final: 0.8789 (tpp) REVERT: A 108 ILE cc_start: 0.9368 (mm) cc_final: 0.9133 (mm) REVERT: A 112 TRP cc_start: 0.8685 (t60) cc_final: 0.8473 (t60) REVERT: A 426 MET cc_start: 0.8334 (ttp) cc_final: 0.6218 (ttp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0563 time to fit residues: 4.6133 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.086 Evaluate side-chains 37 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 536 THR cc_start: 0.8655 (t) cc_final: 0.8447 (t) REVERT: D 537 LEU cc_start: 0.8103 (tp) cc_final: 0.7813 (tp) REVERT: D 539 VAL cc_start: 0.9118 (t) cc_final: 0.8783 (p) REVERT: D 647 GLU cc_start: 0.8868 (pt0) cc_final: 0.8591 (tp30) REVERT: D 653 GLN cc_start: 0.9010 (tm-30) cc_final: 0.7786 (tm-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0368 time to fit residues: 1.5321 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.033 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 : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 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 : 0.000 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 8 optimal weight: 0.0170 chunk 119 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 95 optimal weight: 0.0670 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 652 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059473 restraints weight = 14899.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061165 restraints weight = 8465.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062751 restraints weight = 5855.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063890 restraints weight = 4280.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064690 restraints weight = 3327.829| |-----------------------------------------------------------------------------| r_work (final): 0.3060 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.067642 restraints weight = 4433.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069220 restraints weight = 2519.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070399 restraints weight = 1692.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071033 restraints weight = 1275.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071584 restraints weight = 1067.750| |-----------------------------------------------------------------------------| r_work (final): 0.3169 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.058679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.052507 restraints weight = 333.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.053523 restraints weight = 100.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.054104 restraints weight = 64.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.054415 restraints weight = 51.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.054418 restraints weight = 45.870| |-----------------------------------------------------------------------------| r_work (final): 0.2803 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2136 r_free = 0.2136 target = 0.035186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.035165 restraints weight = 240.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.035165 restraints weight = 0.238 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.035165 restraints weight = 0.237 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.035165 restraints weight = 0.237 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.035165 restraints weight = 0.237 | |-----------------------------------------------------------------------------| r_work (final): 0.2193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15453 Z= 0.189 Angle : 0.919 20.557 21174 Z= 0.437 Chirality : 0.055 0.579 2658 Planarity : 0.005 0.052 2499 Dihedral : 6.065 34.252 1818 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1683 helix: 0.64 (0.26), residues: 369 sheet: -0.04 (0.22), residues: 492 loop : -0.51 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 166 TYR 0.012 0.002 TYR C 217 PHE 0.011 0.001 PHE E 159 TRP 0.085 0.005 TRP A 96 HIS 0.010 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (15315) covalent geometry : angle 0.80046 / 0.41 (20793) SS BOND : bond 0.00585 / 0.36 ( 33) SS BOND : angle 1.41491 / 0.94 ( 66) hydrogen bonds : bond 0.06093 / 4.05 ( 555) hydrogen bonds : angle 5.75175 / 4.05 ( 1827) link_ALPHA1-3 : bond 0.00507 / 0.25 ( 3) link_ALPHA1-3 : angle 1.29340 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00955 / 0.48 ( 3) link_ALPHA1-6 : angle 1.64273 / 1.11 ( 9) link_BETA1-4 : bond 0.00277 / 0.16 ( 33) link_BETA1-4 : angle 1.35070 / 0.93 ( 99) link_NAG-ASN : bond 0.00382 / 0.27 ( 66) link_NAG-ASN : angle 4.60033 / 3.51 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.156 Fit side-chains REVERT: A 86 LEU cc_start: 0.9151 (mm) cc_final: 0.8795 (mm) REVERT: A 98 ASN cc_start: 0.9208 (t0) cc_final: 0.8988 (t0) REVERT: A 104 MET cc_start: 0.9033 (mmm) cc_final: 0.8787 (tpp) REVERT: A 108 ILE cc_start: 0.9327 (mm) cc_final: 0.9104 (mt) REVERT: A 112 TRP cc_start: 0.8646 (t60) cc_final: 0.8434 (t60) REVERT: A 288 LEU cc_start: 0.9188 (mp) cc_final: 0.8966 (mp) REVERT: A 426 MET cc_start: 0.8149 (ttp) cc_final: 0.5823 (ttp) REVERT: A 427 TRP cc_start: 0.7711 (m-90) cc_final: 0.7440 (m-90) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0639 time to fit residues: 5.1704 Evaluate side-chains 48 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.146 Evaluate side-chains 42 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 539 VAL cc_start: 0.9041 (t) cc_final: 0.8744 (p) REVERT: D 591 GLN cc_start: 0.9459 (tt0) cc_final: 0.9257 (tt0) REVERT: D 647 GLU cc_start: 0.8809 (pt0) cc_final: 0.8589 (tp30) REVERT: D 650 GLN cc_start: 0.8670 (tp40) cc_final: 0.7851 (tm-30) REVERT: D 653 GLN cc_start: 0.9011 (tm-30) cc_final: 0.7971 (tm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0575 time to fit residues: 2.6521 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.041 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: 0.0017 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: 0.0009 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 157 optimal weight: 0.0870 chunk 106 optimal weight: 0.0370 chunk 14 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 164 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 575 GLN ** A 293 GLN ** 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 = 0.3235 r_free = 0.3235 target = 0.071712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.060721 restraints weight = 14149.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062589 restraints weight = 8065.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063878 restraints weight = 5395.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064911 restraints weight = 4019.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065618 restraints weight = 3181.138| |-----------------------------------------------------------------------------| r_work (final): 0.3089 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.063920 restraints weight = 4358.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065691 restraints weight = 2527.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066918 restraints weight = 1711.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067805 restraints weight = 1296.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068463 restraints weight = 1047.734| |-----------------------------------------------------------------------------| r_work (final): 0.3111 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.058125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.052235 restraints weight = 361.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.053453 restraints weight = 143.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.054237 restraints weight = 89.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.054819 restraints weight = 67.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.055172 restraints weight = 54.406| |-----------------------------------------------------------------------------| r_work (final): 0.2870 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2049 r_free = 0.2049 target = 0.030489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2050 r_free = 0.2050 target = 0.030369 restraints weight = 191.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2054 r_free = 0.2054 target = 0.030480 restraints weight = 18.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2055 r_free = 0.2055 target = 0.030518 restraints weight = 2.727 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2056 r_free = 0.2056 target = 0.030519 restraints weight = 0.427 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2056 r_free = 0.2056 target = 0.030518 restraints weight = 0.076 | |-----------------------------------------------------------------------------| r_work (final): 0.2049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 15453 Z= 0.202 Angle : 0.939 18.549 21174 Z= 0.452 Chirality : 0.054 0.493 2658 Planarity : 0.005 0.056 2499 Dihedral : 5.873 30.323 1818 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.20), residues: 1683 helix: 0.32 (0.25), residues: 366 sheet: 0.08 (0.22), residues: 465 loop : -0.48 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 588 TYR 0.029 0.003 TYR B 643 PHE 0.008 0.001 PHE A 391 TRP 0.034 0.004 TRP F 571 HIS 0.010 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (15315) covalent geometry : angle 0.84651 / 0.43 (20793) SS BOND : bond 0.00399 / 0.25 ( 33) SS BOND : angle 1.12519 / 0.76 ( 66) hydrogen bonds : bond 0.06140 / 4.08 ( 555) hydrogen bonds : angle 5.54917 / 3.91 ( 1827) link_ALPHA1-3 : bond 0.00584 / 0.29 ( 3) link_ALPHA1-3 : angle 1.34304 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00241 / 0.12 ( 3) link_ALPHA1-6 : angle 1.24152 / 0.84 ( 9) link_BETA1-4 : bond 0.00565 / 0.34 ( 33) link_BETA1-4 : angle 1.42257 / 0.99 ( 99) link_NAG-ASN : bond 0.00328 / 0.23 ( 66) link_NAG-ASN : angle 4.17003 / 3.16 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 86 LEU cc_start: 0.9169 (mm) cc_final: 0.8821 (mm) REVERT: A 95 MET cc_start: 0.8380 (ppp) cc_final: 0.8062 (ppp) REVERT: A 98 ASN cc_start: 0.9360 (t0) cc_final: 0.9091 (t0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0535 time to fit residues: 4.5150 Evaluate side-chains 47 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.148 Evaluate side-chains 44 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 539 VAL cc_start: 0.9119 (t) cc_final: 0.8778 (p) REVERT: B 579 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7508 (ptt180) REVERT: B 589 ASP cc_start: 0.8873 (m-30) cc_final: 0.8641 (m-30) REVERT: B 591 GLN cc_start: 0.9397 (tt0) cc_final: 0.8843 (tt0) REVERT: B 595 ILE cc_start: 0.9460 (tt) cc_final: 0.8793 (tt) REVERT: B 653 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8038 (tm-30) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0501 time to fit residues: 2.4203 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 : 0.039 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 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: 0.0139 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: 168 random chunks: chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 82 optimal weight: 0.0050 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059311 restraints weight = 14892.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061280 restraints weight = 8406.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.062746 restraints weight = 5530.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063756 restraints weight = 4025.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064552 restraints weight = 3157.741| |-----------------------------------------------------------------------------| r_work (final): 0.3065 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065881 restraints weight = 4636.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067627 restraints weight = 2718.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.068938 restraints weight = 1848.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069855 restraints weight = 1389.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070471 restraints weight = 1136.088| |-----------------------------------------------------------------------------| r_work (final): 0.3132 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.059780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055918 restraints weight = 371.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056602 restraints weight = 78.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.057111 restraints weight = 48.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057473 restraints weight = 36.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057674 restraints weight = 29.626| |-----------------------------------------------------------------------------| r_work (final): 0.2912 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2133 r_free = 0.2133 target = 0.040791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2105 r_free = 0.2105 target = 0.039914 restraints weight = 103.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2126 r_free = 0.2126 target = 0.040575 restraints weight = 15.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2131 r_free = 0.2131 target = 0.040708 restraints weight = 3.023 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2133 r_free = 0.2133 target = 0.040777 restraints weight = 0.759 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2133 r_free = 0.2133 target = 0.040777 restraints weight = 0.190 | |-----------------------------------------------------------------------------| r_work (final): 0.2174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 15453 Z= 0.234 Angle : 0.950 18.848 21174 Z= 0.458 Chirality : 0.056 0.439 2658 Planarity : 0.006 0.079 2499 Dihedral : 6.087 33.380 1818 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1683 helix: 0.53 (0.25), residues: 363 sheet: 0.10 (0.22), residues: 465 loop : -0.62 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 308 TYR 0.037 0.003 TYR F 643 PHE 0.012 0.001 PHE E 233 TRP 0.056 0.004 TRP B 610 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (15315) covalent geometry : angle 0.83306 / 0.43 (20793) SS BOND : bond 0.00389 / 0.24 ( 33) SS BOND : angle 1.12893 / 0.73 ( 66) hydrogen bonds : bond 0.06508 / 4.39 ( 555) hydrogen bonds : angle 5.49357 / 3.88 ( 1827) link_ALPHA1-3 : bond 0.00553 / 0.28 ( 3) link_ALPHA1-3 : angle 1.43556 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00481 / 0.24 ( 3) link_ALPHA1-6 : angle 1.33107 / 0.91 ( 9) link_BETA1-4 : bond 0.00384 / 0.23 ( 33) link_BETA1-4 : angle 1.22387 / 0.86 ( 99) link_NAG-ASN : bond 0.00727 / 0.48 ( 66) link_NAG-ASN : angle 4.71848 / 3.58 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7713 (t0) cc_final: 0.6930 (t0) REVERT: A 86 LEU cc_start: 0.9170 (mm) cc_final: 0.8854 (mm) REVERT: A 95 MET cc_start: 0.8844 (ppp) cc_final: 0.8472 (ppp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0486 time to fit residues: 3.8547 Evaluate side-chains 43 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.138 Evaluate side-chains 46 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 537 LEU cc_start: 0.7706 (tp) cc_final: 0.7330 (tp) REVERT: B 589 ASP cc_start: 0.8740 (m-30) cc_final: 0.8492 (m-30) REVERT: B 591 GLN cc_start: 0.9297 (tt0) cc_final: 0.8820 (tt0) REVERT: B 650 GLN cc_start: 0.8776 (tp40) cc_final: 0.8030 (tm-30) REVERT: B 653 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 655 LYS cc_start: 0.8980 (pptt) cc_final: 0.8653 (ptmm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0475 time to fit residues: 2.4361 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 : 0.039 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 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 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 9 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 44 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060148 restraints weight = 14440.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062161 restraints weight = 8186.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063612 restraints weight = 5404.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064633 restraints weight = 3922.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.065424 restraints weight = 3057.840| |-----------------------------------------------------------------------------| r_work (final): 0.3092 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065600 restraints weight = 4399.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067501 restraints weight = 2539.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068773 restraints weight = 1700.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069647 restraints weight = 1280.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070232 restraints weight = 1046.660| |-----------------------------------------------------------------------------| r_work (final): 0.3145 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.060108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.055883 restraints weight = 309.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.057010 restraints weight = 94.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.057742 restraints weight = 57.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.058312 restraints weight = 39.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.058664 restraints weight = 28.293| |-----------------------------------------------------------------------------| r_work (final): 0.2895 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2103 r_free = 0.2103 target = 0.031533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2075 r_free = 0.2075 target = 0.031116 restraints weight = 246.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2095 r_free = 0.2095 target = 0.031384 restraints weight = 32.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2102 r_free = 0.2102 target = 0.031503 restraints weight = 9.001 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2104 r_free = 0.2104 target = 0.031536 restraints weight = 2.793 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2104 r_free = 0.2104 target = 0.031549 restraints weight = 0.988 | |-----------------------------------------------------------------------------| r_work (final): 0.2061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 15453 Z= 0.211 Angle : 0.896 18.630 21174 Z= 0.438 Chirality : 0.055 0.381 2658 Planarity : 0.005 0.057 2499 Dihedral : 6.043 32.060 1818 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1683 helix: 0.58 (0.27), residues: 360 sheet: 0.04 (0.22), residues: 486 loop : -0.56 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 588 TYR 0.039 0.002 TYR F 643 PHE 0.036 0.002 PHE E 210 TRP 0.027 0.003 TRP D 628 HIS 0.008 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (15315) covalent geometry : angle 0.79431 / 0.42 (20793) SS BOND : bond 0.00328 / 0.20 ( 33) SS BOND : angle 1.06488 / 0.70 ( 66) hydrogen bonds : bond 0.06278 / 4.15 ( 555) hydrogen bonds : angle 5.59527 / 3.94 ( 1827) link_ALPHA1-3 : bond 0.00532 / 0.27 ( 3) link_ALPHA1-3 : angle 1.40790 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00455 / 0.23 ( 3) link_ALPHA1-6 : angle 1.40571 / 0.96 ( 9) link_BETA1-4 : bond 0.00564 / 0.34 ( 33) link_BETA1-4 : angle 1.18699 / 0.83 ( 99) link_NAG-ASN : bond 0.00557 / 0.38 ( 66) link_NAG-ASN : angle 4.27480 / 3.26 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.103 Fit side-chains REVERT: A 57 ASP cc_start: 0.8316 (p0) cc_final: 0.8072 (p0) REVERT: A 67 ASN cc_start: 0.7374 (t0) cc_final: 0.7138 (t0) REVERT: A 86 LEU cc_start: 0.9100 (mm) cc_final: 0.8796 (mm) REVERT: A 95 MET cc_start: 0.8910 (ppp) cc_final: 0.8559 (ppp) REVERT: A 426 MET cc_start: 0.8026 (ttm) cc_final: 0.7456 (ttm) REVERT: A 427 TRP cc_start: 0.7625 (m-90) cc_final: 0.7280 (m-90) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0556 time to fit residues: 4.1848 Evaluate side-chains 42 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.148 Evaluate side-chains 38 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 537 LEU cc_start: 0.7452 (tp) cc_final: 0.7228 (tp) REVERT: B 539 VAL cc_start: 0.9329 (m) cc_final: 0.8591 (p) REVERT: B 579 ARG cc_start: 0.8124 (mtp180) cc_final: 0.7395 (ptt180) REVERT: B 589 ASP cc_start: 0.8906 (m-30) cc_final: 0.8647 (m-30) REVERT: B 595 ILE cc_start: 0.9175 (tp) cc_final: 0.8772 (tp) REVERT: B 601 LYS cc_start: 0.8680 (tppp) cc_final: 0.8287 (tppp) REVERT: B 647 GLU cc_start: 0.7986 (tp30) cc_final: 0.7448 (tp30) REVERT: B 653 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8176 (tm-30) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0586 time to fit residues: 2.4561 Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.041 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 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: 0.0010 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: 168 random chunks: chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 140 optimal weight: 0.0020 chunk 73 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 0.0670 chunk 27 optimal weight: 0.0570 chunk 101 optimal weight: 6.9990 overall best weight: 1.5846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 293 GLN ** 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 = 0.3228 r_free = 0.3228 target = 0.070998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059702 restraints weight = 14628.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061714 restraints weight = 8231.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063132 restraints weight = 5439.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.064196 restraints weight = 3972.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064947 restraints weight = 3099.598| |-----------------------------------------------------------------------------| r_work (final): 0.3082 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065133 restraints weight = 4471.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.066874 restraints weight = 2576.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068031 restraints weight = 1754.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068889 restraints weight = 1342.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069407 restraints weight = 1101.768| |-----------------------------------------------------------------------------| r_work (final): 0.3141 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.059236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055118 restraints weight = 424.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.055887 restraints weight = 107.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.056451 restraints weight = 67.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056816 restraints weight = 51.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.057078 restraints weight = 43.087| |-----------------------------------------------------------------------------| r_work (final): 0.2929 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2115 r_free = 0.2115 target = 0.039191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2101 r_free = 0.2101 target = 0.038550 restraints weight = 91.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2116 r_free = 0.2116 target = 0.039129 restraints weight = 14.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2117 r_free = 0.2117 target = 0.039154 restraints weight = 3.134 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2119 r_free = 0.2119 target = 0.039228 restraints weight = 0.717 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2119 r_free = 0.2119 target = 0.039224 restraints weight = 0.164 | |-----------------------------------------------------------------------------| r_work (final): 0.2189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 15453 Z= 0.197 Angle : 0.855 17.285 21174 Z= 0.424 Chirality : 0.053 0.336 2658 Planarity : 0.005 0.042 2499 Dihedral : 5.867 35.236 1818 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1683 helix: 0.65 (0.26), residues: 351 sheet: 0.09 (0.22), residues: 486 loop : -0.55 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 308 TYR 0.038 0.003 TYR D 643 PHE 0.008 0.001 PHE E 233 TRP 0.032 0.003 TRP D 628 HIS 0.005 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (15315) covalent geometry : angle 0.76127 / 0.41 (20793) SS BOND : bond 0.00271 / 0.16 ( 33) SS BOND : angle 0.99915 / 0.64 ( 66) hydrogen bonds : bond 0.06224 / 4.14 ( 555) hydrogen bonds : angle 5.53426 / 3.86 ( 1827) link_ALPHA1-3 : bond 0.00504 / 0.25 ( 3) link_ALPHA1-3 : angle 1.51329 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00309 / 0.15 ( 3) link_ALPHA1-6 : angle 1.30460 / 0.89 ( 9) link_BETA1-4 : bond 0.00260 / 0.16 ( 33) link_BETA1-4 : angle 1.21483 / 0.86 ( 99) link_NAG-ASN : bond 0.00361 / 0.23 ( 66) link_NAG-ASN : angle 4.00726 / 3.05 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.147 Fit side-chains REVERT: A 67 ASN cc_start: 0.7339 (t0) cc_final: 0.7025 (t0) REVERT: A 86 LEU cc_start: 0.9150 (mm) cc_final: 0.8825 (mm) REVERT: A 95 MET cc_start: 0.8944 (ppp) cc_final: 0.8572 (ppp) REVERT: A 161 MET cc_start: 0.8295 (tpt) cc_final: 0.7299 (ppp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0484 time to fit residues: 3.5916 Evaluate side-chains 36 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.208 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 539 VAL cc_start: 0.9397 (m) cc_final: 0.8715 (p) REVERT: B 601 LYS cc_start: 0.8847 (tppp) cc_final: 0.8468 (tppp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0505 time to fit residues: 1.9840 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 : 0.044 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: 0.0020 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: 0.0010 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: 168 random chunks: chunk 96 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 50 optimal weight: 0.0770 chunk 78 optimal weight: 0.3980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 293 GLN B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.061348 restraints weight = 14677.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063404 restraints weight = 8248.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064851 restraints weight = 5475.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.065835 restraints weight = 3962.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066586 restraints weight = 3103.278| |-----------------------------------------------------------------------------| r_work (final): 0.3094 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.065385 restraints weight = 4604.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066993 restraints weight = 2749.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068123 restraints weight = 1888.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.068901 restraints weight = 1446.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069416 restraints weight = 1201.409| |-----------------------------------------------------------------------------| r_work (final): 0.3135 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.062210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.058445 restraints weight = 405.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.059254 restraints weight = 83.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.059838 restraints weight = 49.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060236 restraints weight = 35.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.060417 restraints weight = 26.797| |-----------------------------------------------------------------------------| r_work (final): 0.2965 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1553 r_free = 0.1553 target = 0.018114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.1544 r_free = 0.1544 target = 0.018005 restraints weight = 458.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.1554 r_free = 0.1554 target = 0.018048 restraints weight = 27.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.1556 r_free = 0.1556 target = 0.018075 restraints weight = 7.035 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.1558 r_free = 0.1558 target = 0.018080 restraints weight = 1.829 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.1558 r_free = 0.1558 target = 0.018080 restraints weight = 0.507 | |-----------------------------------------------------------------------------| r_work (final): 0.1574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15453 Z= 0.194 Angle : 0.906 17.669 21174 Z= 0.449 Chirality : 0.055 0.340 2658 Planarity : 0.005 0.041 2499 Dihedral : 5.876 35.035 1818 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.20), residues: 1683 helix: 0.34 (0.26), residues: 357 sheet: -0.02 (0.21), residues: 486 loop : -0.62 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 588 TYR 0.040 0.003 TYR B 643 PHE 0.007 0.001 PHE C 233 TRP 0.046 0.004 TRP B 628 HIS 0.004 0.001 HIS E 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (15315) covalent geometry : angle 0.82792 / 0.43 (20793) SS BOND : bond 0.00221 / 0.13 ( 33) SS BOND : angle 0.91972 / 0.59 ( 66) hydrogen bonds : bond 0.06239 / 4.13 ( 555) hydrogen bonds : angle 5.58577 / 3.93 ( 1827) link_ALPHA1-3 : bond 0.00449 / 0.23 ( 3) link_ALPHA1-3 : angle 1.42457 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00371 / 0.19 ( 3) link_ALPHA1-6 : angle 1.35931 / 0.93 ( 9) link_BETA1-4 : bond 0.00397 / 0.24 ( 33) link_BETA1-4 : angle 1.20880 / 0.85 ( 99) link_NAG-ASN : bond 0.00464 / 0.34 ( 66) link_NAG-ASN : angle 3.83380 / 2.94 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.79 seconds wall clock time: 30 minutes 20.43 seconds (1820.43 seconds total)