Starting phenix.real_space_refine on Sat Jul 4 00:29:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t77_25736/07_2026/7t77_25736.map" } resolution = 4.75 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= 0.010 sd= 0.100 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 105 5.16 5 C 10473 2.51 5 N 2801 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16832 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3518 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 990 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1077 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 812 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: "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: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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: 3.30, per 1000 atoms: 0.20 Number of scatterers: 16832 At special positions: 0 Unit cell: (129.95, 125.35, 165.6, 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 105 16.00 O 3453 8.00 N 2801 7.00 C 10473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.14 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.08 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.16 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 R 3 " - " MAN R 4 " " BMA h 3 " - " MAN h 7 " " MAN h 4 " - " MAN h 5 " " BMA j 3 " - " MAN j 6 " " MAN j 4 " - " MAN j 5 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 6 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 X 2 " - " BMA X 3 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 137 " " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 130 " " NAG A 607 " - " ASN A 133 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 355 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 234 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 185h" " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 137 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN A 156 " " NAG I 1 " - " ASN A 160 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 448 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 448 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 130 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 301 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN E 448 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN E 130 " " NAG j 1 " - " ASN E 156 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 607.5 milliseconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 25 sheets defined 24.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... 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 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.516A pdb=" N LYS B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.588A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.175A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.733A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 460 through 464 removed outlier: 3.760A pdb=" N SER C 463 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 571 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 341 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 460 through 464 removed outlier: 4.273A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.740A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.528A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100I through 100M Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.502A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.595A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.758A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 3.745A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 467 through 470 Processing sheet with id=AB5, first strand: chain 'C' and resid 423 through 425 Processing sheet with id=AB6, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 removed outlier: 5.520A pdb=" N ILE E 215 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY E 250 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR E 217 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'E' and resid 201 through 202 removed outlier: 7.890A pdb=" N GLN E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET E 426 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 302 removed outlier: 7.792A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AC3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.629A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.812A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100O through 103 Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 49 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 19 through 24 480 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 3357 1.32 - 1.47: 6058 1.47 - 1.61: 7591 1.61 - 1.76: 23 1.76 - 1.91: 127 Bond restraints: 17156 Sorted by residual: bond pdb=" CB HIS E 105 " pdb=" CG HIS E 105 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.53e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CB LEU L 106A" pdb=" CG LEU L 106A" ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CB LEU B 663 " pdb=" CG LEU B 663 " ideal model delta sigma weight residual 1.530 1.659 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" NE ARG H 3 " pdb=" CZ ARG H 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.03e+01 ... (remaining 17151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.33: 23251 7.33 - 14.65: 41 14.65 - 21.98: 1 21.98 - 29.31: 0 29.31 - 36.63: 3 Bond angle restraints: 23296 Sorted by residual: angle pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " pdb=" C7 NAG A 601 " ideal model delta sigma weight residual 124.56 161.19 -36.63 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C2 NAG E 605 " pdb=" N2 NAG E 605 " pdb=" C7 NAG E 605 " ideal model delta sigma weight residual 124.56 160.59 -36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" C2 NAG D 702 " pdb=" N2 NAG D 702 " pdb=" C7 NAG D 702 " ideal model delta sigma weight residual 124.56 159.61 -35.05 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C HIS E 72 " pdb=" N ALA E 73 " pdb=" CA ALA E 73 " ideal model delta sigma weight residual 122.84 109.29 13.55 1.30e+00 5.92e-01 1.09e+02 angle pdb=" C GLY E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta sigma weight residual 119.85 128.36 -8.51 1.01e+00 9.80e-01 7.10e+01 ... (remaining 23291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 9048 18.04 - 36.09: 284 36.09 - 54.13: 90 54.13 - 72.17: 33 72.17 - 90.21: 11 Dihedral angle restraints: 9466 sinusoidal: 3828 harmonic: 5638 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 -176.79 -90.21 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 149.44 -56.44 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS D 605 " pdb=" CB CYS D 605 " ideal model delta sinusoidal sigma weight residual 93.00 142.47 -49.47 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 9463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1855 0.107 - 0.214: 642 0.214 - 0.321: 242 0.321 - 0.428: 112 0.428 - 0.535: 62 Chirality restraints: 2913 Sorted by residual: chirality pdb=" C1 MAN R 5 " pdb=" O6 BMA R 3 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.09 0.31 2.00e-02 2.50e+03 2.36e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.68e+02 ... (remaining 2910 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG i 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG j 2 " 0.089 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " 0.526 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.329 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG j 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.210 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4261 2.82 - 3.34: 15821 3.34 - 3.86: 28471 3.86 - 4.38: 34188 4.38 - 4.90: 51974 Nonbonded interactions: 134715 Sorted by model distance: nonbonded pdb=" O TRP E 69 " pdb=" N THR E 71 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS F 574 " model vdw 2.388 3.120 nonbonded pdb=" N GLY A 41 " pdb=" N VAL A 42 " model vdw 2.415 2.560 nonbonded pdb=" N LYS E 97 " pdb=" N ASN E 98 " model vdw 2.418 2.560 nonbonded pdb=" N ASP C 141 " pdb=" OD1 ASP C 141 " model vdw 2.441 3.120 ... (remaining 134710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 32 through 607) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'i' } ncs_group { reference = (chain 'h' and (resid 2 or resid 5 through 7)) selection = (chain 'j' and (resid 1 or resid 4 through 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.030 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.023 0.136 17295 Z= 1.195 Angle : 1.868 36.634 23679 Z= 1.162 Chirality : 0.153 0.535 2913 Planarity : 0.016 0.304 2833 Dihedral : 10.955 82.063 5726 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.71 % Favored : 97.03 % Rotamer: Outliers : 0.87 % Allowed : 0.93 % Favored : 98.20 % Cbeta Deviations : 0.22 % 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: 0.38 (0.19), residues: 1918 helix: -0.47 (0.23), residues: 417 sheet: 0.70 (0.21), residues: 558 loop : 0.50 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 350 TYR 0.054 0.008 TYR C 40 PHE 0.045 0.007 PHE C 93 TRP 0.054 0.008 TRP E 479 HIS 0.010 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.16 (17156) covalent geometry : angle 1.82781 / 1.16 (23296) SS BOND : bond 0.03725 / 2.16 ( 34) SS BOND : angle 3.00027 / 1.99 ( 68) hydrogen bonds : bond 0.15932 / 10.71 ( 480) hydrogen bonds : angle 7.88011 / 5.60 ( 1245) link_ALPHA1-3 : bond 0.03632 / 1.91 ( 5) link_ALPHA1-3 : angle 2.17157 / 1.03 ( 15) link_ALPHA1-6 : bond 0.03867 / 2.03 ( 4) link_ALPHA1-6 : angle 5.07501 / 2.98 ( 12) link_BETA1-4 : bond 0.06823 / 4.10 ( 36) link_BETA1-4 : angle 4.88253 / 3.32 ( 108) link_NAG-ASN : bond 0.07869 / 4.86 ( 60) link_NAG-ASN : angle 2.59678 / 1.80 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9519 (mt) cc_final: 0.9047 (tp) REVERT: A 180 ASP cc_start: 0.8734 (m-30) cc_final: 0.8448 (m-30) REVERT: A 271 ILE cc_start: 0.9434 (mt) cc_final: 0.9209 (tp) REVERT: A 423 ILE cc_start: 0.9118 (mt) cc_final: 0.8756 (mm) REVERT: B 528 SER cc_start: 0.8591 (m) cc_final: 0.7832 (t) REVERT: B 530 MET cc_start: 0.8632 (mtp) cc_final: 0.8383 (mtm) REVERT: B 584 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8987 (tp30) REVERT: B 647 GLU cc_start: 0.8993 (tt0) cc_final: 0.8729 (tm-30) REVERT: B 651 ASN cc_start: 0.8977 (m-40) cc_final: 0.8692 (p0) REVERT: B 654 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7936 (tm-30) REVERT: C 53 PHE cc_start: 0.7880 (m-80) cc_final: 0.7627 (m-10) REVERT: C 101 VAL cc_start: 0.9492 (t) cc_final: 0.9287 (p) REVERT: C 383 PHE cc_start: 0.9129 (m-80) cc_final: 0.8796 (m-80) REVERT: C 384 TYR cc_start: 0.8917 (m-80) cc_final: 0.8440 (m-80) REVERT: D 536 THR cc_start: 0.9269 (p) cc_final: 0.8961 (t) REVERT: D 538 THR cc_start: 0.9005 (p) cc_final: 0.7869 (p) REVERT: D 650 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7901 (tp40) REVERT: E 42 VAL cc_start: 0.9085 (t) cc_final: 0.8671 (t) REVERT: E 69 TRP cc_start: 0.8678 (m-90) cc_final: 0.8287 (m-90) REVERT: E 87 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 98 ASN cc_start: 0.9228 (t0) cc_final: 0.8423 (t0) REVERT: E 478 ASN cc_start: 0.8564 (m-40) cc_final: 0.8359 (m110) REVERT: F 530 MET cc_start: 0.9365 (mtp) cc_final: 0.9051 (mtp) REVERT: F 535 MET cc_start: 0.9067 (mmp) cc_final: 0.8615 (tpp) REVERT: F 540 GLN cc_start: 0.8731 (mm110) cc_final: 0.7989 (mt0) REVERT: F 573 ILE cc_start: 0.8643 (mt) cc_final: 0.8331 (mm) REVERT: F 574 LYS cc_start: 0.8957 (mttt) cc_final: 0.8474 (mtmt) REVERT: F 584 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8865 (tp30) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9348 (mmmt) REVERT: F 643 TYR cc_start: 0.9363 (m-10) cc_final: 0.9010 (m-80) REVERT: F 648 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8549 (tt0) REVERT: F 660 LEU cc_start: 0.8323 (mt) cc_final: 0.8034 (mt) REVERT: H 67 LEU cc_start: 0.8266 (mt) cc_final: 0.8015 (mm) REVERT: H 78 LEU cc_start: 0.9286 (tp) cc_final: 0.9063 (tp) REVERT: H 82 MET cc_start: 0.9002 (ptp) cc_final: 0.8521 (ttt) REVERT: L 4 LEU cc_start: 0.8996 (mt) cc_final: 0.8681 (tt) REVERT: L 36 TYR cc_start: 0.8280 (m-80) cc_final: 0.7901 (m-80) REVERT: L 69 ASN cc_start: 0.8219 (m-40) cc_final: 0.7686 (m-40) REVERT: L 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7443 (m-30) REVERT: L 88 CYS cc_start: 0.3702 (p) cc_final: 0.3078 (p) REVERT: L 96 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8729 (mmt90) outliers start: 15 outliers final: 7 residues processed: 406 average time/residue: 0.1206 time to fit residues: 72.4950 Evaluate side-chains 205 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 585 HIS B 652 GLN B 658 GLN C 66 HIS C 302 ASN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 136 ASN E 195 ASN F 543 ASN H 32 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.043492 restraints weight = 92896.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.045296 restraints weight = 54467.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046603 restraints weight = 37370.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.047525 restraints weight = 28331.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.048230 restraints weight = 23059.149| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17295 Z= 0.201 Angle : 0.859 14.876 23679 Z= 0.413 Chirality : 0.049 0.402 2913 Planarity : 0.005 0.047 2833 Dihedral : 5.534 52.489 2093 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.23 % Allowed : 1.80 % Favored : 97.97 % 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: 0.30 (0.19), residues: 1918 helix: 1.05 (0.26), residues: 372 sheet: 0.28 (0.20), residues: 597 loop : -0.09 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 192 TYR 0.037 0.003 TYR C 484 PHE 0.023 0.002 PHE A 233 TRP 0.029 0.002 TRP L 35 HIS 0.011 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (17156) covalent geometry : angle 0.79061 / 0.40 (23296) SS BOND : bond 0.00435 / 0.27 ( 34) SS BOND : angle 1.29671 / 0.91 ( 68) hydrogen bonds : bond 0.05515 / 3.69 ( 480) hydrogen bonds : angle 6.35112 / 4.51 ( 1245) link_ALPHA1-3 : bond 0.00663 / 0.35 ( 5) link_ALPHA1-3 : angle 1.76550 / 0.96 ( 15) link_ALPHA1-6 : bond 0.01389 / 0.72 ( 4) link_ALPHA1-6 : angle 2.47007 / 1.42 ( 12) link_BETA1-4 : bond 0.00664 / 0.41 ( 36) link_BETA1-4 : angle 3.03974 / 2.06 ( 108) link_NAG-ASN : bond 0.00541 / 0.37 ( 60) link_NAG-ASN : angle 3.06932 / 2.15 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7884 (ptm) cc_final: 0.7665 (ptm) REVERT: A 180 ASP cc_start: 0.9034 (m-30) cc_final: 0.8268 (m-30) REVERT: A 201 ILE cc_start: 0.9313 (mp) cc_final: 0.8544 (tp) REVERT: A 271 ILE cc_start: 0.9296 (mt) cc_final: 0.9033 (tp) REVERT: A 423 ILE cc_start: 0.9036 (mt) cc_final: 0.8627 (mm) REVERT: A 425 ASN cc_start: 0.8462 (p0) cc_final: 0.8105 (p0) REVERT: A 434 MET cc_start: 0.8630 (tpp) cc_final: 0.8203 (tpp) REVERT: A 494 LEU cc_start: 0.8430 (mt) cc_final: 0.7826 (mt) REVERT: B 528 SER cc_start: 0.8585 (m) cc_final: 0.7921 (t) REVERT: B 584 GLU cc_start: 0.9217 (mt-10) cc_final: 0.9001 (tp30) REVERT: B 647 GLU cc_start: 0.9065 (tt0) cc_final: 0.8692 (tm-30) REVERT: B 648 GLU cc_start: 0.9130 (tp30) cc_final: 0.8891 (tp30) REVERT: C 100 MET cc_start: 0.8309 (tpt) cc_final: 0.7978 (mmm) REVERT: C 150 MET cc_start: 0.8735 (mmt) cc_final: 0.8477 (mmm) REVERT: C 186 ARG cc_start: 0.8129 (mmp80) cc_final: 0.7188 (ptm160) REVERT: C 423 ILE cc_start: 0.9147 (mm) cc_final: 0.8928 (tp) REVERT: C 489 VAL cc_start: 0.9009 (m) cc_final: 0.8771 (t) REVERT: D 536 THR cc_start: 0.9069 (p) cc_final: 0.8809 (t) REVERT: D 538 THR cc_start: 0.8670 (p) cc_final: 0.8114 (t) REVERT: D 545 LEU cc_start: 0.8854 (tt) cc_final: 0.8485 (tp) REVERT: D 584 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8846 (tp30) REVERT: D 650 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7738 (tp-100) REVERT: E 42 VAL cc_start: 0.8810 (t) cc_final: 0.8586 (t) REVERT: E 69 TRP cc_start: 0.8550 (m-90) cc_final: 0.8059 (m-10) REVERT: E 98 ASN cc_start: 0.9175 (t0) cc_final: 0.8039 (t0) REVERT: F 530 MET cc_start: 0.9004 (mtp) cc_final: 0.8221 (ttp) REVERT: F 535 MET cc_start: 0.8812 (mmp) cc_final: 0.8408 (tpp) REVERT: F 570 HIS cc_start: 0.6909 (p-80) cc_final: 0.6449 (p-80) REVERT: F 601 LYS cc_start: 0.8963 (mttt) cc_final: 0.8181 (mtmt) REVERT: F 633 LYS cc_start: 0.9696 (mttt) cc_final: 0.9307 (mmmt) REVERT: H 12 VAL cc_start: 0.8459 (m) cc_final: 0.8107 (m) REVERT: H 28 ASP cc_start: 0.8649 (t0) cc_final: 0.8336 (t70) REVERT: H 45 LEU cc_start: 0.9344 (mm) cc_final: 0.8998 (mm) REVERT: H 78 LEU cc_start: 0.9410 (tp) cc_final: 0.9094 (tp) REVERT: H 100 MET cc_start: 0.9250 (mpp) cc_final: 0.8702 (mpp) REVERT: L 36 TYR cc_start: 0.8351 (m-80) cc_final: 0.6916 (m-80) REVERT: L 50 ASP cc_start: 0.8071 (m-30) cc_final: 0.7398 (m-30) REVERT: L 86 TYR cc_start: 0.8648 (m-80) cc_final: 0.8076 (m-80) REVERT: L 104 LEU cc_start: 0.9025 (tp) cc_final: 0.8312 (tp) outliers start: 4 outliers final: 2 residues processed: 252 average time/residue: 0.1088 time to fit residues: 43.5892 Evaluate side-chains 172 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 108 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 169 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN B 651 ASN D 543 ASN D 585 HIS D 591 GLN D 607 ASN D 625 ASN D 650 GLN D 651 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN H 100RHIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.038232 restraints weight = 101511.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.039816 restraints weight = 60937.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.040972 restraints weight = 42722.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.041806 restraints weight = 33042.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.042406 restraints weight = 27302.107| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17295 Z= 0.296 Angle : 0.900 10.772 23679 Z= 0.433 Chirality : 0.049 0.462 2913 Planarity : 0.006 0.142 2833 Dihedral : 5.723 51.253 2093 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.17 % Allowed : 2.85 % Favored : 96.98 % 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: -0.31 (0.19), residues: 1918 helix: 0.55 (0.26), residues: 372 sheet: -0.12 (0.21), residues: 579 loop : -0.46 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 327 TYR 0.024 0.003 TYR L 30 PHE 0.018 0.003 PHE H 100J TRP 0.026 0.003 TRP L 35 HIS 0.009 0.002 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.30 (17156) covalent geometry : angle 0.85388 / 0.42 (23296) SS BOND : bond 0.00477 / 0.30 ( 34) SS BOND : angle 1.54027 / 1.07 ( 68) hydrogen bonds : bond 0.05122 / 3.34 ( 480) hydrogen bonds : angle 6.28239 / 4.42 ( 1245) link_ALPHA1-3 : bond 0.00509 / 0.28 ( 5) link_ALPHA1-3 : angle 2.00667 / 1.14 ( 15) link_ALPHA1-6 : bond 0.01284 / 0.66 ( 4) link_ALPHA1-6 : angle 2.25425 / 1.16 ( 12) link_BETA1-4 : bond 0.00556 / 0.29 ( 36) link_BETA1-4 : angle 2.58628 / 1.74 ( 108) link_NAG-ASN : bond 0.00498 / 0.35 ( 60) link_NAG-ASN : angle 2.57279 / 1.79 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8334 (m-10) cc_final: 0.8086 (m-10) REVERT: A 95 MET cc_start: 0.8095 (ptm) cc_final: 0.7739 (ptm) REVERT: A 98 ASN cc_start: 0.9477 (t0) cc_final: 0.9145 (t0) REVERT: A 180 ASP cc_start: 0.8936 (m-30) cc_final: 0.8082 (m-30) REVERT: A 201 ILE cc_start: 0.9480 (mp) cc_final: 0.8847 (tp) REVERT: A 423 ILE cc_start: 0.9058 (mt) cc_final: 0.8787 (mm) REVERT: A 425 ASN cc_start: 0.8320 (p0) cc_final: 0.7870 (p0) REVERT: B 584 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8707 (tm-30) REVERT: B 626 MET cc_start: 0.8725 (mmp) cc_final: 0.8054 (mmm) REVERT: B 638 TYR cc_start: 0.8082 (t80) cc_final: 0.7724 (t80) REVERT: B 647 GLU cc_start: 0.9432 (tt0) cc_final: 0.8929 (tm-30) REVERT: B 651 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8916 (p0) REVERT: B 657 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8649 (mt-10) REVERT: C 100 MET cc_start: 0.8365 (tpt) cc_final: 0.8047 (tpt) REVERT: C 104 MET cc_start: 0.9050 (ttm) cc_final: 0.8831 (ttt) REVERT: C 150 MET cc_start: 0.9067 (mmt) cc_final: 0.8826 (mmm) REVERT: C 186 ARG cc_start: 0.8197 (mmp80) cc_final: 0.7250 (ptm160) REVERT: D 536 THR cc_start: 0.9002 (p) cc_final: 0.8794 (t) REVERT: D 626 MET cc_start: 0.9175 (tpp) cc_final: 0.8728 (tpp) REVERT: E 69 TRP cc_start: 0.8688 (m-90) cc_final: 0.8432 (m-90) REVERT: E 167 ASN cc_start: 0.9365 (p0) cc_final: 0.9146 (p0) REVERT: E 434 MET cc_start: 0.8917 (mtp) cc_final: 0.8521 (mtp) REVERT: E 478 ASN cc_start: 0.8589 (t0) cc_final: 0.8347 (t0) REVERT: F 530 MET cc_start: 0.8774 (mtp) cc_final: 0.8449 (mtp) REVERT: F 545 LEU cc_start: 0.8948 (tp) cc_final: 0.8672 (tp) REVERT: F 601 LYS cc_start: 0.9373 (mttt) cc_final: 0.8671 (mtpt) REVERT: F 633 LYS cc_start: 0.9682 (mttt) cc_final: 0.9333 (mmmt) REVERT: F 650 GLN cc_start: 0.7413 (tp40) cc_final: 0.6567 (tp40) REVERT: H 18 LEU cc_start: 0.8627 (tp) cc_final: 0.8404 (tp) REVERT: H 28 ASP cc_start: 0.9036 (t0) cc_final: 0.8458 (m-30) REVERT: H 78 LEU cc_start: 0.9506 (tp) cc_final: 0.9236 (tp) REVERT: H 82 MET cc_start: 0.9053 (ttt) cc_final: 0.8554 (tpt) outliers start: 3 outliers final: 1 residues processed: 188 average time/residue: 0.1067 time to fit residues: 31.7777 Evaluate side-chains 129 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 HIS C 114 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.038039 restraints weight = 96263.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.039660 restraints weight = 56798.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.040821 restraints weight = 39383.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.041648 restraints weight = 30287.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.042231 restraints weight = 25078.580| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17295 Z= 0.208 Angle : 0.748 11.841 23679 Z= 0.361 Chirality : 0.046 0.338 2913 Planarity : 0.004 0.061 2833 Dihedral : 5.545 53.124 2093 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1918 helix: 0.57 (0.27), residues: 378 sheet: -0.14 (0.22), residues: 551 loop : -0.43 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 166 TYR 0.019 0.002 TYR D 643 PHE 0.016 0.002 PHE E 382 TRP 0.016 0.002 TRP D 610 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (17156) covalent geometry : angle 0.69266 / 0.35 (23296) SS BOND : bond 0.00383 / 0.23 ( 34) SS BOND : angle 1.51420 / 0.94 ( 68) hydrogen bonds : bond 0.04448 / 2.91 ( 480) hydrogen bonds : angle 5.87189 / 4.16 ( 1245) link_ALPHA1-3 : bond 0.00512 / 0.28 ( 5) link_ALPHA1-3 : angle 1.79389 / 1.00 ( 15) link_ALPHA1-6 : bond 0.00888 / 0.45 ( 4) link_ALPHA1-6 : angle 2.17158 / 1.10 ( 12) link_BETA1-4 : bond 0.00455 / 0.25 ( 36) link_BETA1-4 : angle 2.31467 / 1.55 ( 108) link_NAG-ASN : bond 0.00472 / 0.32 ( 60) link_NAG-ASN : angle 2.62254 / 1.93 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8385 (m-10) cc_final: 0.8079 (m-10) REVERT: A 95 MET cc_start: 0.8097 (ptm) cc_final: 0.7786 (ptm) REVERT: A 98 ASN cc_start: 0.9436 (t0) cc_final: 0.9058 (t0) REVERT: A 104 MET cc_start: 0.9428 (ttm) cc_final: 0.9103 (ttt) REVERT: A 201 ILE cc_start: 0.9447 (mp) cc_final: 0.8866 (tp) REVERT: A 425 ASN cc_start: 0.8137 (p0) cc_final: 0.7678 (p0) REVERT: A 494 LEU cc_start: 0.8722 (mt) cc_final: 0.7868 (mt) REVERT: B 528 SER cc_start: 0.9209 (m) cc_final: 0.8399 (p) REVERT: B 536 THR cc_start: 0.9079 (m) cc_final: 0.8863 (p) REVERT: B 584 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9109 (tp30) REVERT: B 626 MET cc_start: 0.8305 (mmp) cc_final: 0.7851 (mmm) REVERT: B 647 GLU cc_start: 0.9430 (tt0) cc_final: 0.9065 (tm-30) REVERT: B 651 ASN cc_start: 0.9317 (p0) cc_final: 0.8794 (p0) REVERT: C 186 ARG cc_start: 0.8185 (mmp80) cc_final: 0.7271 (ptm160) REVERT: D 584 GLU cc_start: 0.9314 (tt0) cc_final: 0.8833 (tp30) REVERT: E 69 TRP cc_start: 0.8666 (m-90) cc_final: 0.8142 (m-90) REVERT: E 434 MET cc_start: 0.8892 (mtp) cc_final: 0.8615 (mtp) REVERT: E 453 ILE cc_start: 0.8603 (mm) cc_final: 0.8258 (tp) REVERT: E 478 ASN cc_start: 0.8821 (t0) cc_final: 0.8546 (t0) REVERT: F 530 MET cc_start: 0.8802 (mtp) cc_final: 0.8524 (mtt) REVERT: F 535 MET cc_start: 0.8848 (mmp) cc_final: 0.8525 (tpp) REVERT: F 545 LEU cc_start: 0.8907 (tp) cc_final: 0.8621 (tp) REVERT: F 601 LYS cc_start: 0.9386 (mttt) cc_final: 0.8868 (mtmt) REVERT: F 633 LYS cc_start: 0.9683 (mttt) cc_final: 0.9344 (mmmt) REVERT: F 650 GLN cc_start: 0.7401 (tp40) cc_final: 0.6674 (tp40) REVERT: H 18 LEU cc_start: 0.8507 (tp) cc_final: 0.8094 (tp) REVERT: H 28 ASP cc_start: 0.9029 (t0) cc_final: 0.8547 (m-30) REVERT: H 45 LEU cc_start: 0.9361 (mm) cc_final: 0.9153 (mm) REVERT: H 76 ASP cc_start: 0.8018 (m-30) cc_final: 0.7668 (t0) REVERT: H 78 LEU cc_start: 0.9515 (tp) cc_final: 0.9278 (tp) REVERT: H 100 MET cc_start: 0.9261 (mpp) cc_final: 0.8888 (mpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1053 time to fit residues: 28.4185 Evaluate side-chains 130 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 HIS E 103 GLN E 195 ASN E 374 HIS F 570 HIS L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.039247 restraints weight = 97247.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.040897 restraints weight = 57416.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.042095 restraints weight = 39803.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.042935 restraints weight = 30650.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.043487 restraints weight = 25360.424| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17295 Z= 0.127 Angle : 0.647 12.679 23679 Z= 0.314 Chirality : 0.045 0.275 2913 Planarity : 0.004 0.050 2833 Dihedral : 5.206 53.816 2093 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.12 % Allowed : 1.57 % Favored : 98.31 % 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: -0.14 (0.19), residues: 1918 helix: 0.70 (0.27), residues: 381 sheet: 0.01 (0.22), residues: 541 loop : -0.38 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.017 0.001 TYR F 586 PHE 0.014 0.001 PHE L 98 TRP 0.012 0.001 TRP C 112 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (17156) covalent geometry : angle 0.60198 / 0.30 (23296) SS BOND : bond 0.00320 / 0.20 ( 34) SS BOND : angle 1.20987 / 0.73 ( 68) hydrogen bonds : bond 0.04023 / 2.60 ( 480) hydrogen bonds : angle 5.48624 / 3.90 ( 1245) link_ALPHA1-3 : bond 0.00645 / 0.34 ( 5) link_ALPHA1-3 : angle 1.77693 / 0.99 ( 15) link_ALPHA1-6 : bond 0.00821 / 0.42 ( 4) link_ALPHA1-6 : angle 1.88139 / 0.94 ( 12) link_BETA1-4 : bond 0.00532 / 0.32 ( 36) link_BETA1-4 : angle 2.14283 / 1.44 ( 108) link_NAG-ASN : bond 0.00354 / 0.22 ( 60) link_NAG-ASN : angle 2.08442 / 1.50 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8307 (m-10) cc_final: 0.8022 (m-10) REVERT: A 95 MET cc_start: 0.7820 (ptm) cc_final: 0.7618 (ptm) REVERT: A 98 ASN cc_start: 0.9359 (t0) cc_final: 0.8986 (t0) REVERT: A 104 MET cc_start: 0.9411 (ttm) cc_final: 0.9116 (ttt) REVERT: A 201 ILE cc_start: 0.9437 (mp) cc_final: 0.8822 (tp) REVERT: A 425 ASN cc_start: 0.8044 (p0) cc_final: 0.7619 (p0) REVERT: A 494 LEU cc_start: 0.8629 (mt) cc_final: 0.7973 (mt) REVERT: B 528 SER cc_start: 0.9200 (m) cc_final: 0.8427 (p) REVERT: B 574 LYS cc_start: 0.9051 (pptt) cc_final: 0.8808 (pptt) REVERT: B 584 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9019 (tp30) REVERT: B 626 MET cc_start: 0.8511 (mmp) cc_final: 0.8014 (mmm) REVERT: B 647 GLU cc_start: 0.9406 (tt0) cc_final: 0.9099 (tm-30) REVERT: C 150 MET cc_start: 0.9079 (mmt) cc_final: 0.8851 (mmm) REVERT: C 186 ARG cc_start: 0.8241 (mmp80) cc_final: 0.7133 (ptm160) REVERT: D 584 GLU cc_start: 0.9308 (tt0) cc_final: 0.8777 (tp30) REVERT: D 610 TRP cc_start: 0.6961 (p90) cc_final: 0.6490 (p90) REVERT: D 626 MET cc_start: 0.9493 (mmp) cc_final: 0.9186 (tpp) REVERT: E 69 TRP cc_start: 0.8490 (m-90) cc_final: 0.7989 (m-90) REVERT: E 279 ASN cc_start: 0.8727 (t0) cc_final: 0.8105 (t0) REVERT: E 434 MET cc_start: 0.8961 (mtp) cc_final: 0.8607 (mtp) REVERT: E 453 ILE cc_start: 0.8534 (mm) cc_final: 0.8190 (tp) REVERT: E 478 ASN cc_start: 0.8827 (t0) cc_final: 0.8560 (t0) REVERT: F 530 MET cc_start: 0.8886 (mtp) cc_final: 0.8195 (ttp) REVERT: F 545 LEU cc_start: 0.8794 (tp) cc_final: 0.8594 (tp) REVERT: F 601 LYS cc_start: 0.9373 (mttt) cc_final: 0.8896 (mtmt) REVERT: F 633 LYS cc_start: 0.9665 (mttt) cc_final: 0.9332 (mmmt) REVERT: H 18 LEU cc_start: 0.8748 (tp) cc_final: 0.8539 (tp) REVERT: H 28 ASP cc_start: 0.8995 (t0) cc_final: 0.8549 (m-30) REVERT: H 45 LEU cc_start: 0.9231 (mm) cc_final: 0.9017 (mm) REVERT: H 75 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9023 (mtmt) REVERT: H 76 ASP cc_start: 0.7995 (m-30) cc_final: 0.7603 (t0) REVERT: H 78 LEU cc_start: 0.9547 (tp) cc_final: 0.9319 (tp) REVERT: L 89 LYS cc_start: 0.9497 (ttpp) cc_final: 0.8841 (tmmt) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.1012 time to fit residues: 29.7453 Evaluate side-chains 136 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 HIS A 352 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 651 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS L 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.035551 restraints weight = 104291.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.036997 restraints weight = 63510.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.038033 restraints weight = 45140.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.038772 restraints weight = 35443.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039266 restraints weight = 29794.345| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 17295 Z= 0.331 Angle : 0.918 11.890 23679 Z= 0.444 Chirality : 0.049 0.326 2913 Planarity : 0.007 0.227 2833 Dihedral : 5.916 53.637 2093 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -0.94 (0.19), residues: 1918 helix: 0.00 (0.26), residues: 381 sheet: -0.52 (0.22), residues: 548 loop : -0.86 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG E 192 TYR 0.024 0.003 TYR A 217 PHE 0.020 0.003 PHE D 522 TRP 0.024 0.003 TRP D 596 HIS 0.008 0.002 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.33 (17156) covalent geometry : angle 0.87613 / 0.44 (23296) SS BOND : bond 0.00534 / 0.30 ( 34) SS BOND : angle 1.79073 / 1.30 ( 68) hydrogen bonds : bond 0.04939 / 3.18 ( 480) hydrogen bonds : angle 6.16428 / 4.37 ( 1245) link_ALPHA1-3 : bond 0.00586 / 0.32 ( 5) link_ALPHA1-3 : angle 1.91813 / 1.08 ( 15) link_ALPHA1-6 : bond 0.00639 / 0.32 ( 4) link_ALPHA1-6 : angle 2.14592 / 1.07 ( 12) link_BETA1-4 : bond 0.00549 / 0.27 ( 36) link_BETA1-4 : angle 2.51338 / 1.66 ( 108) link_NAG-ASN : bond 0.00738 / 0.46 ( 60) link_NAG-ASN : angle 2.40697 / 1.65 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8622 (m-10) cc_final: 0.8254 (m-10) REVERT: A 95 MET cc_start: 0.8061 (ptm) cc_final: 0.7847 (ptm) REVERT: A 104 MET cc_start: 0.9403 (ttm) cc_final: 0.9097 (ttt) REVERT: A 201 ILE cc_start: 0.9495 (mp) cc_final: 0.8946 (tp) REVERT: A 226 LEU cc_start: 0.8854 (tp) cc_final: 0.8652 (tp) REVERT: A 425 ASN cc_start: 0.8029 (p0) cc_final: 0.7437 (p0) REVERT: A 434 MET cc_start: 0.8647 (tpp) cc_final: 0.8387 (tpt) REVERT: B 528 SER cc_start: 0.9329 (m) cc_final: 0.8735 (p) REVERT: B 530 MET cc_start: 0.8543 (tpp) cc_final: 0.7830 (tpp) REVERT: B 584 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8741 (pp20) REVERT: B 601 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8423 (mmmm) REVERT: B 626 MET cc_start: 0.8557 (mmp) cc_final: 0.8225 (mmm) REVERT: B 651 ASN cc_start: 0.9359 (p0) cc_final: 0.8831 (p0) REVERT: C 150 MET cc_start: 0.9200 (mmt) cc_final: 0.8874 (mmm) REVERT: C 186 ARG cc_start: 0.8261 (mmp80) cc_final: 0.7949 (mmp80) REVERT: D 530 MET cc_start: 0.9107 (tmm) cc_final: 0.8849 (tmm) REVERT: D 595 ILE cc_start: 0.9508 (tt) cc_final: 0.9244 (tt) REVERT: D 610 TRP cc_start: 0.7654 (p90) cc_final: 0.7422 (p90) REVERT: D 626 MET cc_start: 0.9495 (mmp) cc_final: 0.9202 (tpp) REVERT: D 650 GLN cc_start: 0.8655 (tp-100) cc_final: 0.7828 (tp-100) REVERT: E 69 TRP cc_start: 0.8686 (m-90) cc_final: 0.8165 (m-90) REVERT: E 165 LEU cc_start: 0.9573 (tp) cc_final: 0.9348 (tp) REVERT: E 279 ASN cc_start: 0.8954 (t0) cc_final: 0.8334 (t0) REVERT: E 434 MET cc_start: 0.8661 (mtp) cc_final: 0.8399 (mtp) REVERT: E 453 ILE cc_start: 0.8804 (mm) cc_final: 0.8497 (tp) REVERT: E 478 ASN cc_start: 0.8984 (t0) cc_final: 0.8767 (t0) REVERT: F 530 MET cc_start: 0.8780 (mtp) cc_final: 0.8493 (mtt) REVERT: F 545 LEU cc_start: 0.9114 (tp) cc_final: 0.8840 (tp) REVERT: F 633 LYS cc_start: 0.9700 (mttt) cc_final: 0.9350 (mmmt) REVERT: F 655 LYS cc_start: 0.9541 (ttmm) cc_final: 0.8893 (ttmm) REVERT: H 18 LEU cc_start: 0.8624 (tp) cc_final: 0.8423 (tp) REVERT: H 28 ASP cc_start: 0.9091 (t0) cc_final: 0.8102 (m-30) REVERT: H 75 LYS cc_start: 0.9430 (mtmt) cc_final: 0.9215 (mtmt) REVERT: H 78 LEU cc_start: 0.9504 (tp) cc_final: 0.9262 (tp) REVERT: L 23 CYS cc_start: 0.4601 (p) cc_final: 0.3880 (p) REVERT: L 88 CYS cc_start: 0.5029 (t) cc_final: 0.4576 (t) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0963 time to fit residues: 24.0526 Evaluate side-chains 116 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 160 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 607 ASN F 570 HIS F 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.038339 restraints weight = 98041.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.039969 restraints weight = 57854.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.041139 restraints weight = 40266.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041978 restraints weight = 31137.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.042597 restraints weight = 25778.693| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17295 Z= 0.120 Angle : 0.676 11.595 23679 Z= 0.326 Chirality : 0.046 0.338 2913 Planarity : 0.005 0.187 2833 Dihedral : 5.329 56.319 2093 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1918 helix: 0.58 (0.27), residues: 381 sheet: -0.26 (0.22), residues: 548 loop : -0.66 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 192 TYR 0.015 0.001 TYR C 191 PHE 0.014 0.001 PHE E 382 TRP 0.023 0.002 TRP L 35 HIS 0.007 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17156) covalent geometry : angle 0.63211 / 0.32 (23296) SS BOND : bond 0.00354 / 0.22 ( 34) SS BOND : angle 1.10607 / 0.77 ( 68) hydrogen bonds : bond 0.03989 / 2.55 ( 480) hydrogen bonds : angle 5.41844 / 3.88 ( 1245) link_ALPHA1-3 : bond 0.00712 / 0.38 ( 5) link_ALPHA1-3 : angle 1.86114 / 1.01 ( 15) link_ALPHA1-6 : bond 0.00795 / 0.40 ( 4) link_ALPHA1-6 : angle 1.29111 / 0.64 ( 12) link_BETA1-4 : bond 0.00550 / 0.33 ( 36) link_BETA1-4 : angle 2.06671 / 1.38 ( 108) link_NAG-ASN : bond 0.00401 / 0.27 ( 60) link_NAG-ASN : angle 2.23788 / 1.55 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8419 (m-10) cc_final: 0.8171 (m-10) REVERT: A 104 MET cc_start: 0.9392 (ttm) cc_final: 0.9122 (ttt) REVERT: A 201 ILE cc_start: 0.9435 (mp) cc_final: 0.8907 (tp) REVERT: A 425 ASN cc_start: 0.7953 (p0) cc_final: 0.7511 (p0) REVERT: A 494 LEU cc_start: 0.8641 (mt) cc_final: 0.7838 (mt) REVERT: B 528 SER cc_start: 0.9361 (m) cc_final: 0.8879 (p) REVERT: B 530 MET cc_start: 0.8270 (tpp) cc_final: 0.7748 (tpp) REVERT: B 536 THR cc_start: 0.8971 (m) cc_final: 0.8762 (p) REVERT: B 584 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8901 (tp30) REVERT: B 626 MET cc_start: 0.8586 (mmp) cc_final: 0.8072 (mmm) REVERT: B 647 GLU cc_start: 0.9352 (pp20) cc_final: 0.9054 (pp20) REVERT: C 150 MET cc_start: 0.9141 (mmt) cc_final: 0.8895 (mmm) REVERT: C 186 ARG cc_start: 0.8257 (mmp80) cc_final: 0.7331 (ptm160) REVERT: D 584 GLU cc_start: 0.9281 (tt0) cc_final: 0.8671 (tp30) REVERT: D 626 MET cc_start: 0.9448 (mmp) cc_final: 0.9206 (tpp) REVERT: D 633 LYS cc_start: 0.9505 (ptpp) cc_final: 0.9236 (pttm) REVERT: D 650 GLN cc_start: 0.8604 (tp-100) cc_final: 0.7777 (tp-100) REVERT: E 69 TRP cc_start: 0.8435 (m-90) cc_final: 0.7861 (m-10) REVERT: E 279 ASN cc_start: 0.8804 (t0) cc_final: 0.8220 (t0) REVERT: E 434 MET cc_start: 0.8738 (mtp) cc_final: 0.8510 (mtp) REVERT: E 453 ILE cc_start: 0.8626 (mm) cc_final: 0.8340 (tp) REVERT: E 478 ASN cc_start: 0.8964 (t0) cc_final: 0.8542 (t0) REVERT: E 479 TRP cc_start: 0.9103 (m-90) cc_final: 0.8288 (m-90) REVERT: F 530 MET cc_start: 0.8814 (mtp) cc_final: 0.8282 (ttm) REVERT: F 607 ASN cc_start: 0.8925 (p0) cc_final: 0.8618 (p0) REVERT: F 633 LYS cc_start: 0.9668 (mttt) cc_final: 0.9316 (mmmt) REVERT: F 650 GLN cc_start: 0.7915 (tp40) cc_final: 0.7142 (tm-30) REVERT: H 28 ASP cc_start: 0.9045 (t0) cc_final: 0.8579 (m-30) REVERT: H 34 MET cc_start: 0.9434 (mmp) cc_final: 0.8731 (mmm) REVERT: H 75 LYS cc_start: 0.9440 (mtmt) cc_final: 0.9212 (mtmt) REVERT: H 100 MET cc_start: 0.9130 (mpp) cc_final: 0.8856 (mpp) REVERT: L 23 CYS cc_start: 0.4132 (p) cc_final: 0.3655 (p) REVERT: L 35 TRP cc_start: 0.8187 (m100) cc_final: 0.7325 (m100) REVERT: L 75 ILE cc_start: 0.9025 (mp) cc_final: 0.8407 (tp) REVERT: L 88 CYS cc_start: 0.3705 (t) cc_final: 0.3407 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.0979 time to fit residues: 28.1183 Evaluate side-chains 132 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 35 optimal weight: 0.0370 chunk 88 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 651 ASN B 658 GLN D 651 ASN F 570 HIS L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.050138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.038136 restraints weight = 100793.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.039712 restraints weight = 59965.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.040855 restraints weight = 42053.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.041662 restraints weight = 32654.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042238 restraints weight = 27246.344| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17295 Z= 0.140 Angle : 0.651 9.673 23679 Z= 0.316 Chirality : 0.045 0.259 2913 Planarity : 0.007 0.299 2833 Dihedral : 5.258 55.466 2093 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.39 (0.19), residues: 1918 helix: 0.83 (0.28), residues: 378 sheet: -0.27 (0.22), residues: 558 loop : -0.61 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG E 192 TYR 0.019 0.001 TYR F 586 PHE 0.010 0.001 PHE E 382 TRP 0.015 0.001 TRP L 35 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (17156) covalent geometry : angle 0.60837 / 0.31 (23296) SS BOND : bond 0.00319 / 0.19 ( 34) SS BOND : angle 1.11123 / 0.72 ( 68) hydrogen bonds : bond 0.03860 / 2.46 ( 480) hydrogen bonds : angle 5.40404 / 3.87 ( 1245) link_ALPHA1-3 : bond 0.00647 / 0.35 ( 5) link_ALPHA1-3 : angle 1.86586 / 1.06 ( 15) link_ALPHA1-6 : bond 0.00634 / 0.32 ( 4) link_ALPHA1-6 : angle 1.41689 / 0.69 ( 12) link_BETA1-4 : bond 0.00470 / 0.28 ( 36) link_BETA1-4 : angle 2.01771 / 1.35 ( 108) link_NAG-ASN : bond 0.00338 / 0.22 ( 60) link_NAG-ASN : angle 2.13821 / 1.49 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8477 (m-10) cc_final: 0.8160 (m-10) REVERT: A 104 MET cc_start: 0.9403 (ttm) cc_final: 0.9136 (ttt) REVERT: A 201 ILE cc_start: 0.9422 (mp) cc_final: 0.8855 (tp) REVERT: A 425 ASN cc_start: 0.7951 (p0) cc_final: 0.7529 (p0) REVERT: A 434 MET cc_start: 0.8653 (tpp) cc_final: 0.8379 (tpp) REVERT: A 494 LEU cc_start: 0.8723 (mt) cc_final: 0.7841 (mt) REVERT: B 528 SER cc_start: 0.9357 (m) cc_final: 0.8894 (p) REVERT: B 584 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8880 (tp30) REVERT: B 626 MET cc_start: 0.8541 (mmp) cc_final: 0.8063 (mmm) REVERT: B 647 GLU cc_start: 0.9365 (pp20) cc_final: 0.9102 (pp20) REVERT: C 186 ARG cc_start: 0.8283 (mmp80) cc_final: 0.7869 (mmp80) REVERT: C 475 MET cc_start: 0.8845 (mmp) cc_final: 0.7930 (mmp) REVERT: D 584 GLU cc_start: 0.9275 (tt0) cc_final: 0.8702 (tp30) REVERT: D 595 ILE cc_start: 0.9312 (tp) cc_final: 0.8890 (tp) REVERT: D 610 TRP cc_start: 0.7204 (p90) cc_final: 0.6456 (p90) REVERT: D 647 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8815 (mm-30) REVERT: D 650 GLN cc_start: 0.8624 (tp-100) cc_final: 0.7638 (tp-100) REVERT: E 69 TRP cc_start: 0.8446 (m-90) cc_final: 0.7877 (m-10) REVERT: E 279 ASN cc_start: 0.8823 (t0) cc_final: 0.8273 (t0) REVERT: E 453 ILE cc_start: 0.8655 (mm) cc_final: 0.8363 (tp) REVERT: E 478 ASN cc_start: 0.8937 (t0) cc_final: 0.8506 (t0) REVERT: E 479 TRP cc_start: 0.9199 (m-90) cc_final: 0.8344 (m-90) REVERT: F 530 MET cc_start: 0.8723 (mtp) cc_final: 0.8364 (mtt) REVERT: F 633 LYS cc_start: 0.9670 (mttt) cc_final: 0.9317 (mmmt) REVERT: F 650 GLN cc_start: 0.8080 (tp40) cc_final: 0.7468 (tp40) REVERT: F 655 LYS cc_start: 0.9624 (ttmm) cc_final: 0.8943 (ttmm) REVERT: H 28 ASP cc_start: 0.9040 (t0) cc_final: 0.8112 (m-30) REVERT: H 34 MET cc_start: 0.9509 (mmp) cc_final: 0.8861 (mmm) REVERT: H 45 LEU cc_start: 0.9458 (mm) cc_final: 0.9227 (mm) REVERT: L 23 CYS cc_start: 0.3953 (p) cc_final: 0.3695 (p) REVERT: L 35 TRP cc_start: 0.8357 (m100) cc_final: 0.7447 (m100) REVERT: L 75 ILE cc_start: 0.8972 (mp) cc_final: 0.8242 (tp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1021 time to fit residues: 27.8585 Evaluate side-chains 129 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 591 GLN D 651 ASN F 570 HIS L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.037691 restraints weight = 100738.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.039271 restraints weight = 59833.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.040404 restraints weight = 41908.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.041215 restraints weight = 32561.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.041788 restraints weight = 27126.638| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17295 Z= 0.156 Angle : 0.659 10.872 23679 Z= 0.320 Chirality : 0.045 0.473 2913 Planarity : 0.006 0.255 2833 Dihedral : 5.254 55.906 2093 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.44 (0.19), residues: 1918 helix: 0.84 (0.28), residues: 375 sheet: -0.32 (0.22), residues: 551 loop : -0.65 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 192 TYR 0.023 0.002 TYR E 217 PHE 0.012 0.001 PHE E 353 TRP 0.025 0.002 TRP D 596 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (17156) covalent geometry : angle 0.61785 / 0.31 (23296) SS BOND : bond 0.00335 / 0.20 ( 34) SS BOND : angle 1.07875 / 0.72 ( 68) hydrogen bonds : bond 0.03868 / 2.48 ( 480) hydrogen bonds : angle 5.37952 / 3.85 ( 1245) link_ALPHA1-3 : bond 0.00585 / 0.31 ( 5) link_ALPHA1-3 : angle 1.88176 / 1.07 ( 15) link_ALPHA1-6 : bond 0.00627 / 0.32 ( 4) link_ALPHA1-6 : angle 1.43861 / 0.70 ( 12) link_BETA1-4 : bond 0.00444 / 0.26 ( 36) link_BETA1-4 : angle 2.00402 / 1.34 ( 108) link_NAG-ASN : bond 0.00320 / 0.22 ( 60) link_NAG-ASN : angle 2.12683 / 1.45 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8519 (m-10) cc_final: 0.8230 (m-10) REVERT: A 98 ASN cc_start: 0.9306 (t0) cc_final: 0.9002 (t0) REVERT: A 104 MET cc_start: 0.9418 (ttm) cc_final: 0.9148 (ttt) REVERT: A 201 ILE cc_start: 0.9402 (mp) cc_final: 0.8829 (tp) REVERT: A 425 ASN cc_start: 0.7958 (p0) cc_final: 0.7529 (p0) REVERT: B 528 SER cc_start: 0.9329 (m) cc_final: 0.8886 (p) REVERT: B 530 MET cc_start: 0.8667 (tpp) cc_final: 0.7893 (tpp) REVERT: B 584 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8875 (tp30) REVERT: B 601 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8127 (mmmm) REVERT: B 626 MET cc_start: 0.8441 (mmp) cc_final: 0.7967 (mmm) REVERT: B 647 GLU cc_start: 0.9308 (pp20) cc_final: 0.9057 (pp20) REVERT: C 150 MET cc_start: 0.9033 (mmp) cc_final: 0.8822 (mmt) REVERT: C 186 ARG cc_start: 0.8348 (mmp80) cc_final: 0.7921 (mmp80) REVERT: C 475 MET cc_start: 0.8799 (mmp) cc_final: 0.7983 (mmp) REVERT: D 530 MET cc_start: 0.8988 (tmm) cc_final: 0.8757 (tmm) REVERT: D 584 GLU cc_start: 0.9302 (tt0) cc_final: 0.8722 (tp30) REVERT: D 610 TRP cc_start: 0.7176 (p90) cc_final: 0.6620 (p90) REVERT: D 650 GLN cc_start: 0.8680 (tp-100) cc_final: 0.7708 (tp-100) REVERT: E 69 TRP cc_start: 0.8485 (m-90) cc_final: 0.7959 (m-10) REVERT: E 279 ASN cc_start: 0.8853 (t0) cc_final: 0.8254 (t0) REVERT: E 453 ILE cc_start: 0.8711 (mm) cc_final: 0.8401 (tp) REVERT: E 478 ASN cc_start: 0.8977 (t0) cc_final: 0.8509 (t0) REVERT: E 479 TRP cc_start: 0.9198 (m-90) cc_final: 0.8413 (m-90) REVERT: F 530 MET cc_start: 0.8706 (mtp) cc_final: 0.8375 (mtt) REVERT: F 545 LEU cc_start: 0.9017 (tp) cc_final: 0.8745 (tp) REVERT: F 633 LYS cc_start: 0.9674 (mttt) cc_final: 0.9322 (mmmt) REVERT: F 650 GLN cc_start: 0.7911 (tp40) cc_final: 0.7505 (tp40) REVERT: F 655 LYS cc_start: 0.9613 (ttmm) cc_final: 0.8866 (ttmm) REVERT: F 660 LEU cc_start: 0.8049 (mm) cc_final: 0.7740 (pp) REVERT: H 28 ASP cc_start: 0.9064 (t0) cc_final: 0.8146 (m-30) REVERT: H 34 MET cc_start: 0.9519 (mmp) cc_final: 0.8728 (mmm) REVERT: H 45 LEU cc_start: 0.9446 (mm) cc_final: 0.9102 (mm) REVERT: L 23 CYS cc_start: 0.4200 (p) cc_final: 0.3915 (p) REVERT: L 35 TRP cc_start: 0.8428 (m100) cc_final: 0.7589 (m100) REVERT: L 75 ILE cc_start: 0.9001 (mp) cc_final: 0.8203 (tp) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0982 time to fit residues: 26.8407 Evaluate side-chains 126 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN D 591 GLN D 651 ASN F 570 HIS L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.037835 restraints weight = 96384.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.039444 restraints weight = 56644.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.040599 restraints weight = 39244.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.041426 restraints weight = 30165.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.042034 restraints weight = 24899.397| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17295 Z= 0.140 Angle : 0.646 10.781 23679 Z= 0.316 Chirality : 0.045 0.300 2913 Planarity : 0.006 0.236 2833 Dihedral : 5.178 56.405 2093 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.35 (0.20), residues: 1918 helix: 0.86 (0.28), residues: 375 sheet: -0.24 (0.23), residues: 527 loop : -0.57 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 192 TYR 0.024 0.001 TYR F 586 PHE 0.009 0.001 PHE E 382 TRP 0.048 0.002 TRP D 596 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17156) covalent geometry : angle 0.60923 / 0.31 (23296) SS BOND : bond 0.00324 / 0.19 ( 34) SS BOND : angle 1.00353 / 0.68 ( 68) hydrogen bonds : bond 0.03848 / 2.47 ( 480) hydrogen bonds : angle 5.32663 / 3.81 ( 1245) link_ALPHA1-3 : bond 0.00589 / 0.32 ( 5) link_ALPHA1-3 : angle 1.89951 / 1.08 ( 15) link_ALPHA1-6 : bond 0.00649 / 0.33 ( 4) link_ALPHA1-6 : angle 1.38855 / 0.68 ( 12) link_BETA1-4 : bond 0.00470 / 0.27 ( 36) link_BETA1-4 : angle 1.92938 / 1.29 ( 108) link_NAG-ASN : bond 0.00312 / 0.21 ( 60) link_NAG-ASN : angle 1.94610 / 1.36 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8522 (m-10) cc_final: 0.8242 (m-10) REVERT: A 98 ASN cc_start: 0.9284 (t0) cc_final: 0.9025 (t0) REVERT: A 104 MET cc_start: 0.9420 (ttm) cc_final: 0.9150 (ttt) REVERT: A 150 MET cc_start: 0.8890 (ptp) cc_final: 0.8603 (ptt) REVERT: A 201 ILE cc_start: 0.9402 (mp) cc_final: 0.8877 (tp) REVERT: A 425 ASN cc_start: 0.7928 (p0) cc_final: 0.7508 (p0) REVERT: A 494 LEU cc_start: 0.8764 (mt) cc_final: 0.7899 (mt) REVERT: B 528 SER cc_start: 0.9315 (m) cc_final: 0.9046 (t) REVERT: B 530 MET cc_start: 0.8674 (tpp) cc_final: 0.8007 (tpp) REVERT: B 584 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8908 (tp30) REVERT: B 601 LYS cc_start: 0.8403 (mmtm) cc_final: 0.7472 (mtmm) REVERT: B 626 MET cc_start: 0.8375 (mmp) cc_final: 0.7762 (mmm) REVERT: B 647 GLU cc_start: 0.9347 (pp20) cc_final: 0.9083 (pp20) REVERT: C 150 MET cc_start: 0.9050 (mmp) cc_final: 0.8840 (mmt) REVERT: C 186 ARG cc_start: 0.8347 (mmp80) cc_final: 0.7900 (mmp80) REVERT: C 475 MET cc_start: 0.8739 (mmp) cc_final: 0.8513 (mmm) REVERT: D 530 MET cc_start: 0.8993 (tmm) cc_final: 0.8738 (tmm) REVERT: D 584 GLU cc_start: 0.9294 (tt0) cc_final: 0.8769 (tp30) REVERT: D 610 TRP cc_start: 0.7431 (p90) cc_final: 0.6830 (p90) REVERT: D 626 MET cc_start: 0.9176 (tpp) cc_final: 0.8833 (tpp) REVERT: D 650 GLN cc_start: 0.8694 (tp-100) cc_final: 0.7715 (tp-100) REVERT: E 69 TRP cc_start: 0.8552 (m-90) cc_final: 0.8002 (m-10) REVERT: E 103 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8681 (tp-100) REVERT: E 104 MET cc_start: 0.9399 (mmt) cc_final: 0.9175 (mmp) REVERT: E 279 ASN cc_start: 0.8865 (t0) cc_final: 0.8305 (t0) REVERT: E 434 MET cc_start: 0.8724 (mtt) cc_final: 0.8070 (mtm) REVERT: E 453 ILE cc_start: 0.8693 (mm) cc_final: 0.8395 (tp) REVERT: E 478 ASN cc_start: 0.9012 (t0) cc_final: 0.8521 (t0) REVERT: E 479 TRP cc_start: 0.9251 (m-90) cc_final: 0.8459 (m-90) REVERT: F 530 MET cc_start: 0.8676 (mtp) cc_final: 0.8353 (mtt) REVERT: F 633 LYS cc_start: 0.9683 (mttt) cc_final: 0.9349 (mmmt) REVERT: F 650 GLN cc_start: 0.8078 (tp40) cc_final: 0.7474 (tp40) REVERT: F 655 LYS cc_start: 0.9631 (ttmm) cc_final: 0.8909 (ttmm) REVERT: H 28 ASP cc_start: 0.9043 (t0) cc_final: 0.8109 (m-30) REVERT: H 45 LEU cc_start: 0.9529 (mm) cc_final: 0.9162 (mm) REVERT: L 23 CYS cc_start: 0.4247 (p) cc_final: 0.4037 (p) REVERT: L 35 TRP cc_start: 0.8433 (m100) cc_final: 0.7600 (m100) REVERT: L 75 ILE cc_start: 0.8992 (mp) cc_final: 0.8209 (tp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0965 time to fit residues: 26.7110 Evaluate side-chains 130 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 49 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 2 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 651 ASN E 428 GLN F 570 HIS L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.037152 restraints weight = 103188.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.038663 restraints weight = 62132.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.039713 restraints weight = 43849.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.040504 restraints weight = 34387.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.041070 restraints weight = 28760.894| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17295 Z= 0.196 Angle : 0.707 11.689 23679 Z= 0.344 Chirality : 0.045 0.263 2913 Planarity : 0.006 0.226 2833 Dihedral : 5.388 57.076 2093 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.55 (0.19), residues: 1918 helix: 0.73 (0.27), residues: 378 sheet: -0.38 (0.22), residues: 524 loop : -0.71 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 192 TYR 0.038 0.002 TYR D 638 PHE 0.012 0.002 PHE H 91 TRP 0.025 0.002 TRP D 596 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (17156) covalent geometry : angle 0.67095 / 0.34 (23296) SS BOND : bond 0.00346 / 0.20 ( 34) SS BOND : angle 1.09415 / 0.74 ( 68) hydrogen bonds : bond 0.04016 / 2.58 ( 480) hydrogen bonds : angle 5.42649 / 3.87 ( 1245) link_ALPHA1-3 : bond 0.00504 / 0.26 ( 5) link_ALPHA1-3 : angle 2.10975 / 1.21 ( 15) link_ALPHA1-6 : bond 0.00590 / 0.30 ( 4) link_ALPHA1-6 : angle 1.62884 / 0.79 ( 12) link_BETA1-4 : bond 0.00424 / 0.24 ( 36) link_BETA1-4 : angle 2.02097 / 1.35 ( 108) link_NAG-ASN : bond 0.00375 / 0.26 ( 60) link_NAG-ASN : angle 2.02126 / 1.41 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1987.01 seconds wall clock time: 35 minutes 43.86 seconds (2143.86 seconds total)