Starting phenix.real_space_refine on Fri Sep 27 21:23:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/09_2024/7t77_25736.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/09_2024/7t77_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/09_2024/7t77_25736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/09_2024/7t77_25736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/09_2024/7t77_25736.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t77_25736/09_2024/7t77_25736.cif" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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 dihedrals: 21 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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 21 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 dihedrals: 9 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 dihedrals: 27 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 dihedrals: 9 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 dihedrals: 21 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.87, per 1000 atoms: 0.59 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: 5.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.84 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: 4.82 Time building geometry restraints manager: 5.96 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 - 21.61: 11169 21.61 - 43.21: 278 43.21 - 64.82: 86 64.82 - 86.43: 71 86.43 - 108.04: 33 Dihedral angle restraints: 11637 sinusoidal: 5999 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 11634 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 502 or resid 601 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: 3.560 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.630 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.136 17156 Z= 1.386 Angle : 1.828 36.634 23296 Z= 1.161 Chirality : 0.153 0.535 2913 Planarity : 0.016 0.304 2833 Dihedral : 13.668 108.037 7897 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.054 0.008 TRP E 479 HIS 0.010 0.002 HIS A 374 PHE 0.045 0.007 PHE C 93 TYR 0.054 0.008 TYR C 40 ARG 0.010 0.001 ARG C 350 *********************** 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 fitting. rotamer outliers: 15 poor density : 392 time to evaluate : 1.794 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: 0.9049 (tp) REVERT: A 180 ASP cc_start: 0.8734 (m-30) cc_final: 0.8443 (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: 0.8755 (mm) REVERT: B 528 SER cc_start: 0.8591 (m) cc_final: 0.7830 (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: 0.8939 (tp30) REVERT: B 647 GLU cc_start: 0.8993 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 651 ASN cc_start: 0.8977 (m-40) cc_final: 0.8690 (p0) REVERT: B 654 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7934 (tm-30) REVERT: C 53 PHE cc_start: 0.7879 (m-80) cc_final: 0.7627 (m-10) REVERT: C 101 VAL cc_start: 0.9492 (t) cc_final: 0.9286 (p) REVERT: C 383 PHE cc_start: 0.9129 (m-80) cc_final: 0.8804 (m-80) REVERT: C 384 TYR cc_start: 0.8917 (m-80) cc_final: 0.8440 (m-80) REVERT: C 424 ILE cc_start: 0.8785 (mt) cc_final: 0.8583 (mm) REVERT: D 536 THR cc_start: 0.9269 (p) cc_final: 0.8962 (t) REVERT: D 538 THR cc_start: 0.9005 (p) cc_final: 0.7872 (p) REVERT: D 650 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7904 (tp40) REVERT: E 42 VAL cc_start: 0.9085 (t) cc_final: 0.8673 (t) REVERT: E 69 TRP cc_start: 0.8678 (m-90) cc_final: 0.8294 (m-90) REVERT: E 87 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7801 (tm-30) REVERT: E 98 ASN cc_start: 0.9228 (t0) cc_final: 0.8431 (t0) REVERT: E 254 VAL cc_start: 0.9475 (t) cc_final: 0.9233 (p) REVERT: F 530 MET cc_start: 0.9365 (mtp) cc_final: 0.9047 (mtp) REVERT: F 535 MET cc_start: 0.9067 (mmp) cc_final: 0.8619 (tpp) REVERT: F 540 GLN cc_start: 0.8731 (mm110) cc_final: 0.8004 (mt0) REVERT: F 573 ILE cc_start: 0.8643 (mt) cc_final: 0.8334 (mm) REVERT: F 574 LYS cc_start: 0.8958 (mttt) cc_final: 0.8475 (mtmt) REVERT: F 584 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8871 (tp30) REVERT: F 633 LYS cc_start: 0.9686 (mttt) cc_final: 0.9346 (mmmt) REVERT: F 643 TYR cc_start: 0.9363 (m-10) cc_final: 0.9009 (m-80) REVERT: F 648 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8551 (tt0) REVERT: F 660 LEU cc_start: 0.8323 (mt) cc_final: 0.8029 (mt) REVERT: H 28 ASP cc_start: 0.8808 (t0) cc_final: 0.8297 (t0) REVERT: H 67 LEU cc_start: 0.8266 (mt) cc_final: 0.8016 (mm) REVERT: H 78 LEU cc_start: 0.9286 (tp) cc_final: 0.9046 (tp) REVERT: H 82 MET cc_start: 0.9002 (ptp) cc_final: 0.8520 (ttt) REVERT: H 91 PHE cc_start: 0.9263 (m-80) cc_final: 0.8933 (m-80) REVERT: L 4 LEU cc_start: 0.8996 (mt) cc_final: 0.8675 (tt) REVERT: L 36 TYR cc_start: 0.8280 (m-80) cc_final: 0.7911 (m-80) REVERT: L 69 ASN cc_start: 0.8219 (m-40) cc_final: 0.7683 (m-40) REVERT: L 78 LEU cc_start: 0.8730 (tp) cc_final: 0.8527 (tt) REVERT: L 82 ASP cc_start: 0.8194 (m-30) cc_final: 0.7463 (m-30) REVERT: L 88 CYS cc_start: 0.3702 (p) cc_final: 0.3100 (p) REVERT: L 96 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8662 (mmt90) outliers start: 15 outliers final: 6 residues processed: 406 average time/residue: 0.3053 time to fit residues: 179.7954 Evaluate side-chains 207 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.0170 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 HIS B 652 GLN B 658 GLN C 66 HIS ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 136 ASN E 195 ASN F 543 ASN L 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17156 Z= 0.251 Angle : 0.778 13.704 23296 Z= 0.391 Chirality : 0.050 0.386 2913 Planarity : 0.004 0.047 2833 Dihedral : 11.210 81.112 4264 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.35 % Allowed : 1.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1918 helix: 1.01 (0.26), residues: 372 sheet: 0.32 (0.20), residues: 597 loop : -0.06 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.012 0.001 HIS A 190 PHE 0.025 0.002 PHE A 233 TYR 0.038 0.002 TYR C 484 ARG 0.007 0.001 ARG C 192 *********************** 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 268 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 2.058 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: A 180 ASP cc_start: 0.8941 (m-30) cc_final: 0.8151 (m-30) REVERT: A 201 ILE cc_start: 0.9358 (mp) cc_final: 0.8782 (tp) REVERT: A 271 ILE cc_start: 0.9329 (mt) cc_final: 0.9104 (tp) REVERT: A 423 ILE cc_start: 0.8917 (mt) cc_final: 0.8438 (mm) REVERT: A 425 ASN cc_start: 0.8535 (p0) cc_final: 0.8176 (p0) REVERT: A 491 ILE cc_start: 0.9214 (tp) cc_final: 0.8847 (tp) REVERT: A 494 LEU cc_start: 0.8390 (mt) cc_final: 0.8046 (mt) REVERT: B 528 SER cc_start: 0.8710 (m) cc_final: 0.7995 (t) REVERT: B 574 LYS cc_start: 0.9065 (pptt) cc_final: 0.8790 (tmtt) REVERT: B 647 GLU cc_start: 0.8976 (tt0) cc_final: 0.8762 (tm-30) REVERT: C 186 ARG cc_start: 0.7897 (mmp80) cc_final: 0.7364 (ptm160) REVERT: C 217 TYR cc_start: 0.7251 (m-10) cc_final: 0.6936 (m-10) REVERT: C 423 ILE cc_start: 0.8894 (mm) cc_final: 0.8692 (tp) REVERT: C 489 VAL cc_start: 0.9043 (m) cc_final: 0.8834 (t) REVERT: D 536 THR cc_start: 0.9087 (p) cc_final: 0.8862 (t) REVERT: D 538 THR cc_start: 0.8639 (p) cc_final: 0.8170 (t) REVERT: D 584 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8883 (tp30) REVERT: D 650 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7692 (tp-100) REVERT: D 653 GLN cc_start: 0.9020 (pp30) cc_final: 0.8820 (pp30) REVERT: E 42 VAL cc_start: 0.8815 (t) cc_final: 0.8613 (t) REVERT: E 69 TRP cc_start: 0.8421 (m-90) cc_final: 0.7970 (m-10) REVERT: E 98 ASN cc_start: 0.9296 (t0) cc_final: 0.8288 (t0) REVERT: E 475 MET cc_start: 0.7897 (mtp) cc_final: 0.7396 (mtp) REVERT: F 530 MET cc_start: 0.9357 (mtp) cc_final: 0.8992 (mtp) REVERT: F 535 MET cc_start: 0.8964 (mmp) cc_final: 0.8436 (tpp) REVERT: F 570 HIS cc_start: 0.7669 (p-80) cc_final: 0.7404 (p90) REVERT: F 633 LYS cc_start: 0.9712 (mttt) cc_final: 0.9337 (mmmt) REVERT: H 12 VAL cc_start: 0.8585 (m) cc_final: 0.8280 (m) REVERT: H 28 ASP cc_start: 0.8766 (t0) cc_final: 0.8506 (t70) REVERT: H 45 LEU cc_start: 0.9171 (mm) cc_final: 0.8774 (mm) REVERT: H 53 ASP cc_start: 0.8775 (p0) cc_final: 0.8475 (p0) REVERT: H 78 LEU cc_start: 0.9286 (tp) cc_final: 0.9055 (tp) REVERT: H 82 ASN cc_start: 0.8277 (m-40) cc_final: 0.8030 (p0) REVERT: H 100 MET cc_start: 0.9289 (mpp) cc_final: 0.8866 (mpp) REVERT: L 36 TYR cc_start: 0.8295 (m-80) cc_final: 0.6832 (m-80) REVERT: L 50 ASP cc_start: 0.8025 (m-30) cc_final: 0.7411 (m-30) REVERT: L 69 ASN cc_start: 0.8289 (m-40) cc_final: 0.7642 (m-40) REVERT: L 86 TYR cc_start: 0.8399 (m-80) cc_final: 0.7840 (m-80) REVERT: L 89 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8857 (ttpt) REVERT: L 92 THR cc_start: 0.8508 (p) cc_final: 0.8289 (t) REVERT: L 104 LEU cc_start: 0.8756 (tt) cc_final: 0.8383 (tt) outliers start: 6 outliers final: 2 residues processed: 267 average time/residue: 0.2555 time to fit residues: 106.4954 Evaluate side-chains 179 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 302 ASN D 543 ASN D 585 HIS D 591 GLN D 625 ASN D 651 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100RHIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17156 Z= 0.315 Angle : 0.741 9.166 23296 Z= 0.370 Chirality : 0.048 0.341 2913 Planarity : 0.004 0.044 2833 Dihedral : 9.178 74.966 4264 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1918 helix: 0.83 (0.27), residues: 372 sheet: -0.03 (0.21), residues: 580 loop : -0.20 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 35 HIS 0.007 0.002 HIS A 190 PHE 0.021 0.002 PHE H 100J TYR 0.022 0.003 TYR D 643 ARG 0.008 0.001 ARG D 617 *********************** 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 201 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.900 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: A 98 ASN cc_start: 0.9458 (t0) cc_final: 0.9198 (t0) REVERT: A 180 ASP cc_start: 0.8915 (m-30) cc_final: 0.8039 (m-30) REVERT: A 201 ILE cc_start: 0.9500 (mp) cc_final: 0.8956 (tp) REVERT: A 423 ILE cc_start: 0.8973 (mt) cc_final: 0.8621 (mm) REVERT: A 425 ASN cc_start: 0.8440 (p0) cc_final: 0.8106 (p0) REVERT: A 494 LEU cc_start: 0.8738 (mt) cc_final: 0.8135 (mt) REVERT: B 626 MET cc_start: 0.8741 (mmp) cc_final: 0.8156 (mmm) REVERT: B 647 GLU cc_start: 0.9315 (tt0) cc_final: 0.9047 (tm-30) REVERT: B 648 GLU cc_start: 0.9234 (tp30) cc_final: 0.8961 (tp30) REVERT: B 657 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8627 (mt-10) REVERT: C 150 MET cc_start: 0.9067 (mmp) cc_final: 0.8624 (mmp) REVERT: C 186 ARG cc_start: 0.7869 (mmp80) cc_final: 0.7229 (ptm160) REVERT: C 423 ILE cc_start: 0.9142 (mm) cc_final: 0.8895 (tp) REVERT: D 584 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8943 (tp30) REVERT: E 69 TRP cc_start: 0.8416 (m-90) cc_final: 0.8038 (m-90) REVERT: E 98 ASN cc_start: 0.9403 (t0) cc_final: 0.8729 (t0) REVERT: E 434 MET cc_start: 0.8981 (mtp) cc_final: 0.8632 (mtp) REVERT: F 530 MET cc_start: 0.9216 (mtp) cc_final: 0.8884 (ttm) REVERT: F 535 MET cc_start: 0.9017 (mmp) cc_final: 0.8491 (tpp) REVERT: F 601 LYS cc_start: 0.9316 (mttt) cc_final: 0.8750 (mtmt) REVERT: F 633 LYS cc_start: 0.9708 (mttt) cc_final: 0.9354 (mmmt) REVERT: F 650 GLN cc_start: 0.7240 (tp40) cc_final: 0.6583 (tp40) REVERT: H 28 ASP cc_start: 0.8871 (t0) cc_final: 0.8196 (m-30) REVERT: H 45 LEU cc_start: 0.9363 (mm) cc_final: 0.9025 (mm) REVERT: H 53 ASP cc_start: 0.8835 (p0) cc_final: 0.8529 (p0) REVERT: H 78 LEU cc_start: 0.9392 (tp) cc_final: 0.9186 (tp) REVERT: H 82 MET cc_start: 0.8934 (ttt) cc_final: 0.8573 (tpt) REVERT: H 100 MET cc_start: 0.9404 (mpp) cc_final: 0.9028 (mpp) REVERT: L 4 LEU cc_start: 0.8700 (tt) cc_final: 0.8379 (tt) REVERT: L 6 GLN cc_start: 0.6694 (mt0) cc_final: 0.5607 (mp10) REVERT: L 88 CYS cc_start: 0.4537 (p) cc_final: 0.3487 (p) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2605 time to fit residues: 82.1774 Evaluate side-chains 147 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17156 Z= 0.200 Angle : 0.627 9.882 23296 Z= 0.317 Chirality : 0.047 0.329 2913 Planarity : 0.004 0.108 2833 Dihedral : 7.810 69.087 4264 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.19), residues: 1918 helix: 0.83 (0.27), residues: 378 sheet: 0.02 (0.21), residues: 585 loop : -0.24 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.005 0.001 HIS A 190 PHE 0.011 0.001 PHE E 382 TYR 0.021 0.002 TYR D 643 ARG 0.012 0.000 ARG A 327 *********************** 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 196 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.9416 (t0) cc_final: 0.9151 (t0) REVERT: A 104 MET cc_start: 0.9247 (ttt) cc_final: 0.9031 (ttt) REVERT: A 180 ASP cc_start: 0.8699 (m-30) cc_final: 0.7673 (m-30) REVERT: A 201 ILE cc_start: 0.9476 (mp) cc_final: 0.8909 (tp) REVERT: A 423 ILE cc_start: 0.8817 (mt) cc_final: 0.8569 (mm) REVERT: A 425 ASN cc_start: 0.8334 (p0) cc_final: 0.7983 (p0) REVERT: A 494 LEU cc_start: 0.8734 (mt) cc_final: 0.8215 (mt) REVERT: B 626 MET cc_start: 0.8342 (mmp) cc_final: 0.8007 (mmm) REVERT: C 104 MET cc_start: 0.9061 (ttm) cc_final: 0.8815 (ttm) REVERT: C 150 MET cc_start: 0.9176 (mmp) cc_final: 0.8762 (mmp) REVERT: C 186 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7289 (ptm160) REVERT: D 584 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8957 (tp30) REVERT: D 610 TRP cc_start: 0.6721 (p90) cc_final: 0.6514 (p90) REVERT: D 626 MET cc_start: 0.9274 (tpp) cc_final: 0.8990 (tpp) REVERT: E 69 TRP cc_start: 0.8349 (m-90) cc_final: 0.7923 (m-90) REVERT: E 98 ASN cc_start: 0.9433 (t0) cc_final: 0.8866 (t0) REVERT: E 434 MET cc_start: 0.8890 (mtp) cc_final: 0.8612 (mtp) REVERT: E 453 ILE cc_start: 0.8497 (mm) cc_final: 0.8217 (tp) REVERT: F 530 MET cc_start: 0.9246 (mtp) cc_final: 0.8577 (ttp) REVERT: F 535 MET cc_start: 0.8887 (mmp) cc_final: 0.8525 (tpp) REVERT: F 601 LYS cc_start: 0.9327 (mttt) cc_final: 0.9032 (mtmt) REVERT: F 633 LYS cc_start: 0.9682 (mttt) cc_final: 0.9359 (mmmt) REVERT: F 650 GLN cc_start: 0.7083 (tp40) cc_final: 0.6456 (tp40) REVERT: H 28 ASP cc_start: 0.8831 (t0) cc_final: 0.8284 (m-30) REVERT: H 45 LEU cc_start: 0.9277 (mm) cc_final: 0.8877 (mm) REVERT: H 53 ASP cc_start: 0.8843 (p0) cc_final: 0.8505 (p0) REVERT: H 78 LEU cc_start: 0.9397 (tp) cc_final: 0.9179 (tp) REVERT: H 82 MET cc_start: 0.8944 (ttt) cc_final: 0.8488 (tpt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2611 time to fit residues: 79.5964 Evaluate side-chains 146 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS B 591 GLN C 114 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17156 Z= 0.310 Angle : 0.708 9.751 23296 Z= 0.356 Chirality : 0.047 0.322 2913 Planarity : 0.005 0.051 2833 Dihedral : 7.564 66.842 4264 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1918 helix: 0.65 (0.27), residues: 378 sheet: -0.27 (0.22), residues: 559 loop : -0.45 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.008 0.001 HIS C 85 PHE 0.016 0.002 PHE H 91 TYR 0.022 0.002 TYR B 638 ARG 0.014 0.001 ARG F 617 *********************** 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 178 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.910 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: 0.8228 (m-10) cc_final: 0.7995 (m-10) REVERT: A 201 ILE cc_start: 0.9514 (mp) cc_final: 0.9142 (tp) REVERT: A 425 ASN cc_start: 0.8259 (p0) cc_final: 0.7846 (p0) REVERT: A 434 MET cc_start: 0.8740 (tpp) cc_final: 0.8481 (tpp) REVERT: B 536 THR cc_start: 0.9026 (m) cc_final: 0.8819 (p) REVERT: B 647 GLU cc_start: 0.9206 (tt0) cc_final: 0.8963 (tt0) REVERT: B 648 GLU cc_start: 0.9179 (tp30) cc_final: 0.8958 (tp30) REVERT: B 651 ASN cc_start: 0.9460 (p0) cc_final: 0.9227 (p0) REVERT: B 655 LYS cc_start: 0.9341 (pttt) cc_final: 0.9134 (pptt) REVERT: C 150 MET cc_start: 0.9193 (mmp) cc_final: 0.8775 (mmp) REVERT: C 186 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7370 (ptm160) REVERT: D 626 MET cc_start: 0.9302 (tpp) cc_final: 0.9084 (tpp) REVERT: D 650 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7621 (tp-100) REVERT: E 69 TRP cc_start: 0.8416 (m-90) cc_final: 0.7933 (m-10) REVERT: E 98 ASN cc_start: 0.9408 (t0) cc_final: 0.8856 (t0) REVERT: E 279 ASN cc_start: 0.8885 (t0) cc_final: 0.8181 (t0) REVERT: E 453 ILE cc_start: 0.8703 (mm) cc_final: 0.8441 (tp) REVERT: F 530 MET cc_start: 0.9222 (mtp) cc_final: 0.8973 (mtt) REVERT: F 535 MET cc_start: 0.8817 (mmp) cc_final: 0.8497 (tpp) REVERT: F 545 LEU cc_start: 0.8960 (tp) cc_final: 0.8759 (tp) REVERT: F 601 LYS cc_start: 0.9521 (mttt) cc_final: 0.9203 (mtmt) REVERT: F 633 LYS cc_start: 0.9698 (mttt) cc_final: 0.9397 (mmmt) REVERT: F 650 GLN cc_start: 0.7420 (tp40) cc_final: 0.6615 (tp40) REVERT: H 28 ASP cc_start: 0.8794 (t0) cc_final: 0.8163 (m-30) REVERT: H 45 LEU cc_start: 0.9486 (mm) cc_final: 0.9212 (mm) REVERT: H 53 ASP cc_start: 0.8931 (p0) cc_final: 0.8583 (p0) REVERT: H 75 LYS cc_start: 0.9503 (mtmt) cc_final: 0.9208 (mtmt) REVERT: H 82 MET cc_start: 0.8933 (ttt) cc_final: 0.8605 (tpt) REVERT: L 23 CYS cc_start: 0.5340 (p) cc_final: 0.3788 (p) REVERT: L 35 TRP cc_start: 0.8378 (m100) cc_final: 0.7526 (m100) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2684 time to fit residues: 74.7478 Evaluate side-chains 129 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 86 optimal weight: 0.0030 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17156 Z= 0.155 Angle : 0.573 9.479 23296 Z= 0.292 Chirality : 0.045 0.256 2913 Planarity : 0.004 0.057 2833 Dihedral : 6.996 62.019 4264 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.06 % Allowed : 0.93 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1918 helix: 0.48 (0.26), residues: 399 sheet: 0.04 (0.22), residues: 546 loop : -0.37 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 479 HIS 0.007 0.001 HIS E 249 PHE 0.010 0.001 PHE A 93 TYR 0.014 0.001 TYR F 586 ARG 0.004 0.000 ARG E 186 *********************** 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 191 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8047 (m-10) cc_final: 0.7802 (m-10) REVERT: A 201 ILE cc_start: 0.9494 (mp) cc_final: 0.8981 (tp) REVERT: A 425 ASN cc_start: 0.8121 (p0) cc_final: 0.7723 (p0) REVERT: A 434 MET cc_start: 0.8698 (tpp) cc_final: 0.8453 (tpp) REVERT: A 494 LEU cc_start: 0.8795 (mt) cc_final: 0.8231 (mt) REVERT: B 528 SER cc_start: 0.9303 (m) cc_final: 0.8543 (p) REVERT: B 626 MET cc_start: 0.8451 (mmp) cc_final: 0.8187 (mmm) REVERT: B 648 GLU cc_start: 0.9124 (tp30) cc_final: 0.8914 (tp30) REVERT: B 655 LYS cc_start: 0.9339 (pttt) cc_final: 0.9100 (pptt) REVERT: C 150 MET cc_start: 0.9254 (mmp) cc_final: 0.8877 (mmp) REVERT: C 186 ARG cc_start: 0.7870 (mmp80) cc_final: 0.7302 (ptm160) REVERT: D 584 GLU cc_start: 0.9058 (tp30) cc_final: 0.8837 (tp30) REVERT: D 626 MET cc_start: 0.9294 (tpp) cc_final: 0.9079 (tpp) REVERT: D 650 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7571 (tp-100) REVERT: E 69 TRP cc_start: 0.8309 (m-90) cc_final: 0.7889 (m-90) REVERT: E 98 ASN cc_start: 0.9288 (t0) cc_final: 0.8899 (t0) REVERT: E 434 MET cc_start: 0.9085 (mtp) cc_final: 0.8745 (mtt) REVERT: E 453 ILE cc_start: 0.8518 (mm) cc_final: 0.8275 (tp) REVERT: E 478 ASN cc_start: 0.9016 (t0) cc_final: 0.8556 (t0) REVERT: E 479 TRP cc_start: 0.9114 (m-90) cc_final: 0.8390 (m-90) REVERT: F 530 MET cc_start: 0.9258 (mtp) cc_final: 0.8611 (ttp) REVERT: F 535 MET cc_start: 0.8810 (mmp) cc_final: 0.8574 (tpp) REVERT: F 601 LYS cc_start: 0.9425 (mttt) cc_final: 0.9085 (mtmt) REVERT: F 633 LYS cc_start: 0.9688 (mttt) cc_final: 0.9355 (mmmt) REVERT: F 650 GLN cc_start: 0.7252 (tp40) cc_final: 0.6497 (tp40) REVERT: F 655 LYS cc_start: 0.9598 (ttmm) cc_final: 0.9189 (ttmm) REVERT: H 28 ASP cc_start: 0.8729 (t0) cc_final: 0.8201 (m-30) REVERT: H 45 LEU cc_start: 0.9431 (mm) cc_final: 0.9118 (mm) REVERT: H 53 ASP cc_start: 0.8893 (p0) cc_final: 0.8446 (p0) REVERT: L 23 CYS cc_start: 0.5535 (p) cc_final: 0.4205 (p) REVERT: L 35 TRP cc_start: 0.8330 (m100) cc_final: 0.7528 (m100) REVERT: L 88 CYS cc_start: 0.5443 (t) cc_final: 0.4247 (t) REVERT: L 89 LYS cc_start: 0.8700 (ttpp) cc_final: 0.8178 (tmmt) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.2525 time to fit residues: 76.9215 Evaluate side-chains 142 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17156 Z= 0.150 Angle : 0.566 9.525 23296 Z= 0.290 Chirality : 0.046 0.389 2913 Planarity : 0.003 0.050 2833 Dihedral : 6.734 61.187 4264 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1918 helix: 0.61 (0.27), residues: 396 sheet: 0.10 (0.22), residues: 567 loop : -0.36 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 479 HIS 0.006 0.001 HIS E 249 PHE 0.013 0.001 PHE L 62 TYR 0.030 0.001 TYR B 638 ARG 0.010 0.000 ARG E 186 *********************** 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 191 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.783 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 201 ILE cc_start: 0.9453 (mp) cc_final: 0.8999 (tp) REVERT: A 425 ASN cc_start: 0.8108 (p0) cc_final: 0.7727 (p0) REVERT: A 494 LEU cc_start: 0.8805 (mt) cc_final: 0.8297 (mt) REVERT: B 528 SER cc_start: 0.9283 (m) cc_final: 0.8541 (p) REVERT: B 626 MET cc_start: 0.8350 (mmp) cc_final: 0.8135 (mmm) REVERT: B 648 GLU cc_start: 0.9217 (tp30) cc_final: 0.8984 (tp30) REVERT: B 655 LYS cc_start: 0.9425 (pttt) cc_final: 0.9181 (pptt) REVERT: C 150 MET cc_start: 0.9239 (mmp) cc_final: 0.8856 (mmp) REVERT: C 186 ARG cc_start: 0.7896 (mmp80) cc_final: 0.7400 (ptm160) REVERT: D 584 GLU cc_start: 0.9115 (tp30) cc_final: 0.8850 (tp30) REVERT: D 626 MET cc_start: 0.9277 (tpp) cc_final: 0.9051 (tpp) REVERT: D 650 GLN cc_start: 0.8519 (tp-100) cc_final: 0.7715 (tp-100) REVERT: E 98 ASN cc_start: 0.9263 (t0) cc_final: 0.8959 (t0) REVERT: E 279 ASN cc_start: 0.8752 (t0) cc_final: 0.8130 (t0) REVERT: E 434 MET cc_start: 0.8376 (mtp) cc_final: 0.8158 (mtm) REVERT: E 453 ILE cc_start: 0.8508 (mm) cc_final: 0.8268 (tp) REVERT: E 478 ASN cc_start: 0.8939 (t0) cc_final: 0.8526 (t0) REVERT: E 479 TRP cc_start: 0.9186 (m-90) cc_final: 0.8335 (m-90) REVERT: F 530 MET cc_start: 0.9238 (mtp) cc_final: 0.8612 (ttp) REVERT: F 535 MET cc_start: 0.8822 (mmp) cc_final: 0.8570 (tpp) REVERT: F 601 LYS cc_start: 0.9430 (mttt) cc_final: 0.9138 (mtmt) REVERT: F 633 LYS cc_start: 0.9693 (mttt) cc_final: 0.9359 (mmmt) REVERT: F 655 LYS cc_start: 0.9656 (ttmm) cc_final: 0.9156 (ttmm) REVERT: H 28 ASP cc_start: 0.8726 (t0) cc_final: 0.8194 (m-30) REVERT: H 45 LEU cc_start: 0.9451 (mm) cc_final: 0.9150 (mm) REVERT: H 53 ASP cc_start: 0.8887 (p0) cc_final: 0.8443 (p0) REVERT: H 76 ASP cc_start: 0.8447 (m-30) cc_final: 0.8093 (t0) REVERT: H 82 MET cc_start: 0.8863 (ttt) cc_final: 0.8538 (tpt) REVERT: L 23 CYS cc_start: 0.5970 (p) cc_final: 0.4081 (p) REVERT: L 35 TRP cc_start: 0.8268 (m100) cc_final: 0.7393 (m100) REVERT: L 88 CYS cc_start: 0.5353 (t) cc_final: 0.4109 (t) REVERT: L 89 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8348 (ttpt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2438 time to fit residues: 74.2638 Evaluate side-chains 143 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 168 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS B 591 GLN D 651 ASN F 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17156 Z= 0.351 Angle : 0.745 9.604 23296 Z= 0.376 Chirality : 0.047 0.288 2913 Planarity : 0.005 0.052 2833 Dihedral : 7.280 59.534 4264 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.19), residues: 1918 helix: 0.19 (0.26), residues: 399 sheet: -0.19 (0.22), residues: 524 loop : -0.60 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 69 HIS 0.011 0.002 HIS E 105 PHE 0.018 0.002 PHE H 100J TYR 0.025 0.002 TYR F 586 ARG 0.004 0.001 ARG E 429 *********************** 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 167 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ILE cc_start: 0.9451 (mp) cc_final: 0.9160 (tp) REVERT: A 425 ASN cc_start: 0.8184 (p0) cc_final: 0.7708 (p0) REVERT: B 528 SER cc_start: 0.9313 (m) cc_final: 0.8711 (p) REVERT: B 626 MET cc_start: 0.8272 (mmp) cc_final: 0.8011 (mmm) REVERT: B 647 GLU cc_start: 0.9163 (tt0) cc_final: 0.8748 (tt0) REVERT: B 648 GLU cc_start: 0.9154 (tp30) cc_final: 0.8948 (tp30) REVERT: B 651 ASN cc_start: 0.9500 (p0) cc_final: 0.9159 (p0) REVERT: C 100 MET cc_start: 0.8786 (mmm) cc_final: 0.8570 (tpt) REVERT: C 150 MET cc_start: 0.9308 (mmp) cc_final: 0.8965 (mmp) REVERT: C 186 ARG cc_start: 0.7980 (mmp80) cc_final: 0.7499 (ptm160) REVERT: C 434 MET cc_start: 0.8074 (ppp) cc_final: 0.7847 (ppp) REVERT: D 584 GLU cc_start: 0.9152 (tp30) cc_final: 0.8878 (tp30) REVERT: D 610 TRP cc_start: 0.6939 (p90) cc_final: 0.6372 (p90) REVERT: D 626 MET cc_start: 0.9248 (tpp) cc_final: 0.8940 (tpp) REVERT: D 650 GLN cc_start: 0.8625 (tp-100) cc_final: 0.7510 (tp-100) REVERT: E 103 GLN cc_start: 0.9250 (tp40) cc_final: 0.8753 (tp-100) REVERT: E 279 ASN cc_start: 0.8955 (t0) cc_final: 0.8383 (t0) REVERT: E 453 ILE cc_start: 0.8773 (mm) cc_final: 0.8540 (tp) REVERT: F 530 MET cc_start: 0.9080 (mtp) cc_final: 0.8784 (mtt) REVERT: F 535 MET cc_start: 0.8923 (mmp) cc_final: 0.8587 (tpp) REVERT: F 545 LEU cc_start: 0.9166 (tp) cc_final: 0.8830 (tp) REVERT: F 633 LYS cc_start: 0.9701 (mttt) cc_final: 0.9395 (mmmt) REVERT: F 650 GLN cc_start: 0.7594 (tp40) cc_final: 0.6682 (tp40) REVERT: F 655 LYS cc_start: 0.9638 (ttmm) cc_final: 0.9037 (ttmm) REVERT: H 45 LEU cc_start: 0.9471 (mm) cc_final: 0.9197 (mm) REVERT: H 53 ASP cc_start: 0.8987 (p0) cc_final: 0.8667 (p0) REVERT: H 76 ASP cc_start: 0.8628 (m-30) cc_final: 0.8176 (t0) REVERT: H 82 MET cc_start: 0.8944 (ttt) cc_final: 0.8639 (tpt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2608 time to fit residues: 68.7550 Evaluate side-chains 123 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 652 GLN D 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17156 Z= 0.162 Angle : 0.599 9.516 23296 Z= 0.305 Chirality : 0.046 0.388 2913 Planarity : 0.004 0.069 2833 Dihedral : 6.807 57.466 4264 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1918 helix: 0.62 (0.27), residues: 384 sheet: -0.12 (0.22), residues: 557 loop : -0.51 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 69 HIS 0.006 0.001 HIS E 249 PHE 0.012 0.001 PHE E 382 TYR 0.030 0.002 TYR B 638 ARG 0.004 0.000 ARG E 273 *********************** 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 181 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.214 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: A 201 ILE cc_start: 0.9442 (mp) cc_final: 0.9085 (tp) REVERT: A 425 ASN cc_start: 0.8018 (p0) cc_final: 0.7606 (p0) REVERT: A 494 LEU cc_start: 0.8882 (mt) cc_final: 0.8262 (mt) REVERT: B 528 SER cc_start: 0.9240 (m) cc_final: 0.8656 (p) REVERT: B 647 GLU cc_start: 0.9205 (tt0) cc_final: 0.8877 (tt0) REVERT: B 648 GLU cc_start: 0.9128 (tp30) cc_final: 0.8859 (tm-30) REVERT: C 150 MET cc_start: 0.9273 (mmp) cc_final: 0.8932 (mmp) REVERT: C 426 MET cc_start: 0.6214 (tpp) cc_final: 0.5869 (tpp) REVERT: D 584 GLU cc_start: 0.9081 (tp30) cc_final: 0.8826 (tp30) REVERT: D 610 TRP cc_start: 0.6888 (p90) cc_final: 0.6385 (p90) REVERT: D 626 MET cc_start: 0.9244 (tpp) cc_final: 0.8927 (tpp) REVERT: D 650 GLN cc_start: 0.8617 (tp-100) cc_final: 0.7677 (tp-100) REVERT: E 69 TRP cc_start: 0.8343 (m-90) cc_final: 0.7866 (m-90) REVERT: E 103 GLN cc_start: 0.9178 (tp40) cc_final: 0.8670 (tp-100) REVERT: E 165 LEU cc_start: 0.9651 (tp) cc_final: 0.9438 (tt) REVERT: E 279 ASN cc_start: 0.8878 (t0) cc_final: 0.8255 (t0) REVERT: E 453 ILE cc_start: 0.8656 (mm) cc_final: 0.8403 (tp) REVERT: F 530 MET cc_start: 0.9155 (mtp) cc_final: 0.8518 (ttp) REVERT: F 535 MET cc_start: 0.8876 (mmp) cc_final: 0.8562 (tpp) REVERT: F 545 LEU cc_start: 0.9039 (tp) cc_final: 0.8796 (tp) REVERT: F 607 ASN cc_start: 0.8907 (p0) cc_final: 0.8632 (p0) REVERT: F 633 LYS cc_start: 0.9690 (mttt) cc_final: 0.9373 (mmmt) REVERT: F 650 GLN cc_start: 0.7400 (tp40) cc_final: 0.6984 (tp-100) REVERT: F 655 LYS cc_start: 0.9668 (ttmm) cc_final: 0.9026 (ttmm) REVERT: H 34 MET cc_start: 0.9347 (mmp) cc_final: 0.8695 (mmm) REVERT: H 45 LEU cc_start: 0.9324 (mm) cc_final: 0.9002 (mm) REVERT: H 53 ASP cc_start: 0.9008 (p0) cc_final: 0.8557 (p0) REVERT: H 76 ASP cc_start: 0.8527 (m-30) cc_final: 0.8101 (t0) REVERT: H 82 MET cc_start: 0.8790 (ttt) cc_final: 0.8480 (tpt) REVERT: H 100 MET cc_start: 0.9459 (mpp) cc_final: 0.8997 (mpp) REVERT: L 35 TRP cc_start: 0.8392 (m100) cc_final: 0.7971 (m100) REVERT: L 88 CYS cc_start: 0.5576 (t) cc_final: 0.4486 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2628 time to fit residues: 77.6409 Evaluate side-chains 136 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 117 optimal weight: 0.0870 chunk 93 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 651 ASN F 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17156 Z= 0.176 Angle : 0.586 9.775 23296 Z= 0.299 Chirality : 0.045 0.290 2913 Planarity : 0.004 0.053 2833 Dihedral : 6.600 57.219 4264 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1918 helix: 0.79 (0.27), residues: 378 sheet: -0.14 (0.22), residues: 551 loop : -0.45 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 69 HIS 0.006 0.001 HIS A 249 PHE 0.008 0.001 PHE E 382 TYR 0.039 0.002 TYR D 638 ARG 0.003 0.000 ARG E 273 ********************** 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 176 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.087 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: A 98 ASN cc_start: 0.9370 (t0) cc_final: 0.8945 (t0) REVERT: A 201 ILE cc_start: 0.9429 (mp) cc_final: 0.9116 (tp) REVERT: A 425 ASN cc_start: 0.8046 (p0) cc_final: 0.7655 (p0) REVERT: A 494 LEU cc_start: 0.8879 (mt) cc_final: 0.8236 (mt) REVERT: B 528 SER cc_start: 0.9194 (m) cc_final: 0.8627 (p) REVERT: C 150 MET cc_start: 0.9282 (mmp) cc_final: 0.8935 (mmp) REVERT: C 186 ARG cc_start: 0.7993 (mmp80) cc_final: 0.7542 (ptm160) REVERT: C 426 MET cc_start: 0.6189 (tpp) cc_final: 0.5847 (tpp) REVERT: C 475 MET cc_start: 0.8915 (mmp) cc_final: 0.7971 (mmp) REVERT: C 482 GLU cc_start: 0.8654 (mp0) cc_final: 0.8402 (mm-30) REVERT: D 610 TRP cc_start: 0.6937 (p90) cc_final: 0.6437 (p90) REVERT: D 626 MET cc_start: 0.9219 (tpp) cc_final: 0.8942 (tpp) REVERT: D 650 GLN cc_start: 0.8639 (tp-100) cc_final: 0.7553 (tp-100) REVERT: E 69 TRP cc_start: 0.8444 (m-90) cc_final: 0.7896 (m-90) REVERT: E 100 MET cc_start: 0.9392 (ptt) cc_final: 0.9068 (ppp) REVERT: E 103 GLN cc_start: 0.9075 (tp40) cc_final: 0.8551 (tp-100) REVERT: E 165 LEU cc_start: 0.9613 (tp) cc_final: 0.9348 (tt) REVERT: E 279 ASN cc_start: 0.8848 (t0) cc_final: 0.8317 (t0) REVERT: E 434 MET cc_start: 0.8270 (mtt) cc_final: 0.8028 (mtt) REVERT: E 453 ILE cc_start: 0.8656 (mm) cc_final: 0.8435 (tp) REVERT: E 478 ASN cc_start: 0.9011 (t0) cc_final: 0.8701 (t0) REVERT: E 479 TRP cc_start: 0.9260 (m-90) cc_final: 0.8472 (m-90) REVERT: F 530 MET cc_start: 0.9113 (mtp) cc_final: 0.8670 (ttm) REVERT: F 535 MET cc_start: 0.8842 (mmp) cc_final: 0.8558 (tpp) REVERT: F 545 LEU cc_start: 0.9076 (tp) cc_final: 0.8869 (tp) REVERT: F 633 LYS cc_start: 0.9698 (mttt) cc_final: 0.9378 (mmmt) REVERT: F 650 GLN cc_start: 0.7139 (tp40) cc_final: 0.6433 (tp40) REVERT: F 655 LYS cc_start: 0.9633 (ttmm) cc_final: 0.9070 (ttmm) REVERT: H 34 MET cc_start: 0.9434 (mmp) cc_final: 0.8846 (mmm) REVERT: H 45 LEU cc_start: 0.9284 (mm) cc_final: 0.8929 (mm) REVERT: H 53 ASP cc_start: 0.8981 (p0) cc_final: 0.8514 (p0) REVERT: H 76 ASP cc_start: 0.8466 (m-30) cc_final: 0.8122 (t0) REVERT: H 82 MET cc_start: 0.8791 (ttt) cc_final: 0.8501 (tpt) REVERT: H 100 MET cc_start: 0.9412 (mpp) cc_final: 0.8846 (mpp) REVERT: L 35 TRP cc_start: 0.8457 (m100) cc_final: 0.8002 (m100) REVERT: L 88 CYS cc_start: 0.5519 (t) cc_final: 0.4604 (t) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2490 time to fit residues: 71.0805 Evaluate side-chains 134 residues out of total 1721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN B 652 GLN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN F 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.049717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.037872 restraints weight = 99832.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.039377 restraints weight = 60662.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.040453 restraints weight = 43085.551| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17156 Z= 0.261 Angle : 0.652 9.653 23296 Z= 0.331 Chirality : 0.045 0.262 2913 Planarity : 0.004 0.054 2833 Dihedral : 6.836 58.068 4264 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1918 helix: 0.60 (0.27), residues: 381 sheet: -0.21 (0.22), residues: 548 loop : -0.59 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.002 TRP A 69 HIS 0.005 0.002 HIS A 374 PHE 0.013 0.002 PHE H 91 TYR 0.023 0.002 TYR F 586 ARG 0.004 0.000 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.98 seconds wall clock time: 54 minutes 28.27 seconds (3268.27 seconds total)